diff --git a/CHANGELOG b/CHANGELOG
index f922eae688a1c3f797e26e48b30ace74c73c024b..1e338b5cbd74da6bc6defd6fa664c64fc2d9be45 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,10 @@
+minerva (12.2.0~alpha.0) stable; urgency=medium
+ * Bug fix: export to CellDesigner align inhibition reaction properly
+ * Bug fix: export/import to/from SBML handles Heterodimer Association
+ reaction properly
+ * Small improvement: export to SBML includes unit factors
+
+
minerva (12.1.1) stable; urgency=medium
* Bug fix: lineWidth in data overlays was ignored
* Bug fix: legend was blinking after using controls
diff --git a/README.md b/README.md
index b251437d1cd86f5c1de174ff3ef4970a79ac4ca3..b568921a6a621bff3f3a6ffcfcf1ab6640c40551 100644
--- a/README.md
+++ b/README.md
@@ -505,7 +505,7 @@ curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" http://pg-sandbox.uni.lu/mine
* Body: the input file to be converted
* Example:
```
-curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" --data @cell_designer.xml -H "Content-Type: text/plain" http://pg-sandbox.uni.lu/minerva/api/convert/CellDesigner_SBML:SBML
+curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" --data-binary @cell_designer.xml -H "Content-Type: text/plain" http://pg-sandbox.uni.lu/minerva/api/convert/CellDesigner_SBML:SBML
```
* Conversion to image
@@ -527,7 +527,7 @@ curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" http://pg-sandbox.uni.lu/mine
* Body: the input file to be converted
* Example:
```
-curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" --data @cell_designer.xml -H "Content-Type: text/plain" http://pg-sandbox.uni.lu/minerva/api/convert/image/CellDesigner_SBML:SVG
+curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" --data-binary @cell_designer.xml -H "Content-Type: text/plain" http://pg-sandbox.uni.lu/minerva/api/convert/image/CellDesigner_SBML:SVG
```
# JavaScript API. Unstable dev API.
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java
index 272366e5235cbb35a1c659af5e50d575cbce2b02..22ef7b50bcdb9731b0cf5fea2edd380a259bad39 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java
@@ -2,6 +2,8 @@ package lcsb.mapviewer.converter.model.celldesigner.geometry;
import java.awt.geom.Point2D;
+import org.apache.log4j.Logger;
+
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
@@ -31,6 +33,12 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
public class CellDesignerAliasConverter implements ICellDesignerAliasConverter<Element> {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CellDesignerAliasConverter.class);
+
/**
* Class helping with transforming objects into meaningful identifiers.
*/
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerAnchor.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerAnchor.java
index 00ac7467700a6475f4ac171c316a1031f199e40a..c80119b1a8b2ee9bb4849af339c01d815df1a534 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerAnchor.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerAnchor.java
@@ -10,136 +10,136 @@ package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
*/
public enum CellDesignerAnchor {
- /**
- * East direction.
- */
- E("E", 0.0),
-
- /**
- * East southeast direction.
- */
- ESE("ESE", 22.5),
-
- /**
- * Southeast direction.
- */
- SE("SE", 45.0),
-
- /**
- * South southeast direction.
- */
- SSE("SSE", 67.5),
-
- /**
- * South direction.
- */
- S("S", 90.0),
-
- /**
- * South southwest direction.
- */
- SSW("SSW", 112.5),
-
- /**
- * Southwest direction.
- */
- SW("SW", 135.0),
-
- /**
- * West southwest direction.
- */
- WSW("WSW", 157.5),
-
- /**
- * West direction.
- */
- W("W", 180.0),
-
- /**
- * West northwest direction.
- */
- WNW("WNW", 202.5),
-
- /**
- * Northwest direction.
- */
- NW("NW", 225.0),
-
- /**
- * North northwest direction.
- */
- NNW("NNW", 247.5),
-
- /**
- * North direction.
- */
- N("N", 270.0),
-
- /**
- * North northeast direction.
- */
- NNE("NNE", 292.5),
-
- /**
- * Northeast direction.
- */
- NE("NE", 315.0),
-
- /**
- * East northeast direction.
- */
- ENE("ENE", 337.5),
-
- /**
- * Unknown direction.
- */
- INACTIVE("INACTIVE", null); // UNDOCUMENTED
-
- /**
- * We have this number of different valid anchors in CellDesigner.
- */
- static final int DIFFERENT_ANCHORS = 16;
-
- /**
- * Name of the anchor.
- */
- private String name;
-
- /**
- * Angle (in radians) on the border where the ancor is localized.
- */
- private Double angle;
-
- /**
- * Default constructor with name and angle value.
- *
- * @param name
- * name of the anchor
- * @param angleDegrees
- * angle (in degrees) on the border where the ancor is localized
- */
- CellDesignerAnchor(String name, Double angleDegrees) {
- this.name = name;
- if (angleDegrees == null) {
- this.angle = null;
- } else {
- this.angle = Math.toRadians(angleDegrees);
- }
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @return the angle
- * @see #angle
- */
- public Double getAngle() {
- return angle;
- }
+ /**
+ * East direction.
+ */
+ E("E", 0.0),
+
+ /**
+ * East south-east direction.
+ */
+ ESE("ESE", 22.5),
+
+ /**
+ * South-east direction.
+ */
+ SE("SE", 45.0),
+
+ /**
+ * South south-east direction.
+ */
+ SSE("SSE", 67.5),
+
+ /**
+ * South direction.
+ */
+ S("S", 90.0),
+
+ /**
+ * South south-west direction.
+ */
+ SSW("SSW", 112.5),
+
+ /**
+ * South-west direction.
+ */
+ SW("SW", 135.0),
+
+ /**
+ * West south-west direction.
+ */
+ WSW("WSW", 157.5),
+
+ /**
+ * West direction.
+ */
+ W("W", 180.0),
+
+ /**
+ * West northwest direction.
+ */
+ WNW("WNW", 202.5),
+
+ /**
+ * Northwest direction.
+ */
+ NW("NW", 225.0),
+
+ /**
+ * North northwest direction.
+ */
+ NNW("NNW", 247.5),
+
+ /**
+ * North direction.
+ */
+ N("N", 270.0),
+
+ /**
+ * North northeast direction.
+ */
+ NNE("NNE", 292.5),
+
+ /**
+ * Northeast direction.
+ */
+ NE("NE", 315.0),
+
+ /**
+ * East northeast direction.
+ */
+ ENE("ENE", 337.5),
+
+ /**
+ * Unknown direction.
+ */
+ INACTIVE("INACTIVE", null); // UNDOCUMENTED
+
+ /**
+ * We have this number of different valid anchors in CellDesigner.
+ */
+ static final int DIFFERENT_ANCHORS = 16;
+
+ /**
+ * Name of the anchor.
+ */
+ private String name;
+
+ /**
+ * Angle (in radians) on the border where the anchor is localized.
+ */
+ private Double angle;
+
+ /**
+ * Default constructor with name and angle value.
+ *
+ * @param name
+ * name of the anchor
+ * @param angleDegrees
+ * angle (in degrees) on the border where the anchor is localized
+ */
+ CellDesignerAnchor(String name, Double angleDegrees) {
+ this.name = name;
+ if (angleDegrees == null) {
+ this.angle = null;
+ } else {
+ this.angle = Math.toRadians(angleDegrees);
+ }
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @return the angle
+ * @see #angle
+ */
+ public Double getAngle() {
+ return angle;
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
index 3a0f31449be24fcb0ef4d0044ef0a8ff5852ad48..4811f185fcd90a39366181136cc76780f71c1416 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
@@ -564,6 +564,9 @@ public class ReactionFromXml extends XmlParser {
num2 = points.size() - 1;
result.getPoints().addAll(points);
}
+ if (num0 == null || num1 == null) {
+ throw new InvalidXmlSchemaException("No information about line separation");
+ }
result.setNum0(num0);
result.setNum1(num1);
result.setNum2(num2);
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
index 04dfa0ab8ad4837e1af75d97c324044ccda6bd01..93b36d3da15633ba9456a0ba187c5a2b79e05347 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
@@ -35,6 +35,7 @@ import lcsb.mapviewer.model.map.reaction.NodeOperator;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
import lcsb.mapviewer.model.map.reaction.type.SimpleReactionInterface;
import lcsb.mapviewer.model.map.reaction.type.TwoProductReactionInterface;
import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
@@ -543,7 +544,7 @@ public class ReactionToXml extends XmlParser {
result.append(" modificationType=\"" + lineData.getCellDesignerString() + "\"");
CellDesignerLineTransformation clt = new CellDesignerLineTransformation();
- List<Point2D> points = clt.getPointsFromLine(product.getLine());
+ List<Point2D> points = clt.getPointsFromLine(getLineBeforeTrimming(product));
result.append(" editPoints=\"");
for (int i = 0; i < points.size(); i++) {
@@ -702,7 +703,7 @@ public class ReactionToXml extends XmlParser {
*/
private String getProductLinkXmlString(Product product) {
Element alias = product.getElement();
- PolylineData[] lines = new PolylineData[] { product.getLine() };
+ PolylineData[] lines = new PolylineData[] { getLineBeforeTrimming(product) };
StringBuilder sb = new StringBuilder();
sb.append("<celldesigner:productLink ");
@@ -711,7 +712,7 @@ public class ReactionToXml extends XmlParser {
// targetLineIndex is missing (maybe it's unimportant :))
sb.append(">\n");
- sb.append(getAnchorXml(alias, product.getLine().getEndPoint()));
+ sb.append(getAnchorXml(alias, getLineBeforeTrimming(product).getEndPoint()));
sb.append(getConnectSchemeXmlStringForLines(lines));
@@ -848,12 +849,13 @@ public class ReactionToXml extends XmlParser {
if (reaction instanceof SimpleReactionInterface) {
Product product = reaction.getProducts().get(0);
Reactant reactant = reaction.getReactants().get(0);
- List<Point2D> points = new ArrayList<Point2D>();
+ List<Point2D> points = new ArrayList<>();
for (int i = 0; i < reactant.getLine().getPoints().size() - 1; i++) {
points.add(reactant.getLine().getPoints().get(i));
}
- for (int i = 1; i < product.getLine().getPoints().size(); i++) {
- points.add(product.getLine().getPoints().get(i));
+ PolylineData productLine = getLineBeforeTrimming(product);
+ for (int i = 1; i < productLine.getPoints().size(); i++) {
+ points.add(productLine.getPoints().get(i));
}
PolylineData pd = new PolylineData(points);
@@ -864,7 +866,7 @@ public class ReactionToXml extends XmlParser {
Reactant reactant2 = reaction.getReactants().get(1);
PolylineData line1 = reactant1.getLine();
PolylineData line2 = reactant2.getLine();
- List<Point2D> points = new ArrayList<Point2D>();
+ List<Point2D> points = new ArrayList<>();
for (NodeOperator operator : reaction.getOperators()) {
if (operator.isReactantOperator()) {
boolean process = true;
@@ -881,8 +883,9 @@ public class ReactionToXml extends XmlParser {
}
}
Product product = reaction.getProducts().get(0);
- for (int i = 1; i < product.getLine().getPoints().size(); i++) {
- points.add(product.getLine().getPoints().get(i));
+ PolylineData productLine = getLineBeforeTrimming(product);
+ for (int i = 1; i < productLine.getPoints().size(); i++) {
+ points.add(productLine.getPoints().get(i));
}
Point2D endPoint = points.get(points.size() - 1);
@@ -945,8 +948,8 @@ public class ReactionToXml extends XmlParser {
PolylineData line1 = new PolylineData(points);
- PolylineData line2 = product1.getLine();
- PolylineData line3 = product2.getLine();
+ PolylineData line2 = getLineBeforeTrimming(product1);
+ PolylineData line3 = getLineBeforeTrimming(product2);
Point2D pointA = product1.getElement().getCenter();
Point2D pointB = product2.getElement().getCenter();
@@ -1032,7 +1035,7 @@ public class ReactionToXml extends XmlParser {
* @return xml node with list of base products
*/
private String getBaseProductsXmlStringForReaction(Reaction reaction) {
- List<Product> products = new ArrayList<Product>();
+ List<Product> products = new ArrayList<>();
products.add(reaction.getProducts().get(0));
if (reaction instanceof TwoProductReactionInterface) {
products.add(reaction.getProducts().get(1));
@@ -1041,12 +1044,12 @@ public class ReactionToXml extends XmlParser {
StringBuilder sb = new StringBuilder();
sb.append("<celldesigner:baseProducts>\n");
for (Product product : products) {
- Element alias = product.getElement();
+ Element element = product.getElement();
sb.append("<celldesigner:baseProduct ");
- sb.append("species=\"" + elements.getElementId(product.getElement()) + "\" ");
- sb.append("alias=\"" + product.getElement().getElementId() + "\" ");
+ sb.append("species=\"" + elements.getElementId(element) + "\" ");
+ sb.append("alias=\"" + element.getElementId() + "\" ");
sb.append(">\n");
- sb.append(getAnchorXml(alias, product.getLine().getEndPoint()));
+ sb.append(getAnchorXml(element, getLineBeforeTrimming(product).getEndPoint()));
sb.append("</celldesigner:baseProduct>\n");
}
@@ -1104,4 +1107,16 @@ public class ReactionToXml extends XmlParser {
}
}
+ private PolylineData getLineBeforeTrimming(ReactionNode node) {
+ if (node instanceof Product) {
+ // line was trimmed for some reaction types
+ PolylineData line = node.getLine().copy();
+ ReactionLineData rld = ReactionLineData.getByReactionType(node.getReaction().getClass());
+ line.trimEnd(-rld.getProductLineTrim());
+ return line;
+ } else {
+ return node.getLine();
+ }
+ }
+
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
index 26242b8fb053fc896f3a7d09f6e612f38c9dc881..ef8ee5eb57546748d8ea574917e8363b7af34fe6 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
@@ -8,6 +8,7 @@ import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import static org.mockito.Mockito.when;
+import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
import java.io.BufferedReader;
@@ -18,6 +19,7 @@ import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.nio.charset.StandardCharsets;
+import java.util.List;
import org.apache.log4j.Logger;
import org.junit.After;
@@ -1011,4 +1013,34 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
throw e;
}
}
+
+ @Test
+ public void testReactionCoordsEqual() throws Exception {
+ try {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/reaction_coords_different.xml"));
+
+ String xmlString = parser.toXml(model);
+ InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is));
+
+ Reaction r1 = model.getReactions().iterator().next();
+ Reaction r2 = model2.getReactions().iterator().next();
+
+ List<Line2D> lines1 = r1.getLines();
+ List<Line2D> lines2 = r2.getLines();
+ for (int i = 0; i < lines1.size(); i++) {
+ Line2D line1 = lines1.get(i);
+ Line2D line2 = lines2.get(i);
+ assertEquals("Distance between points too big:" + line1.getP1() + ";" + line2.getP1(), 0,
+ line1.getP1().distance(line2.getP1()), Configuration.EPSILON);
+ assertEquals("Distance between points too big:" + line1.getP2() + ";" + line2.getP2(), 0,
+ line1.getP2().distance(line2.getP2()), Configuration.EPSILON);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AllGeometryTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AllGeometryTests.java
index 596be399a055313b71a7a5fc065b1105fc3da1fb..09f80e2522d91c611d48ef0eb37bb3e51484f8d2 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AllGeometryTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AllGeometryTests.java
@@ -11,6 +11,7 @@ import org.junit.runners.Suite.SuiteClasses;
AllHelperTests.class,
AntisenseRnaCellDesignerAliasConverterTest.class,
CellDesignerAliasConverterTest.class,
+ ComplexConverterTest.class,
DegradedCellDesignerAliasConverterTest.class,
GeneCellDesignerAliasConverterTest.class,
IonCellDesignerAliasConverterTest.class,
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ComplexConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ComplexConverterTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..fad062832ea8133d82db7cc274c36738a018b51d
--- /dev/null
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ComplexConverterTest.java
@@ -0,0 +1,70 @@
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import static org.junit.Assert.assertEquals;
+
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+
+public class ComplexConverterTest extends CellDesignerTestFunctions {
+ static Logger logger = Logger.getLogger(ComplexConverterTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetAnchorForAlias() throws Exception {
+ try {
+
+ Complex alias = new Complex("id");
+ alias.setWidth(200);
+ alias.setHeight(300);
+ alias.setX(100.0);
+ alias.setY(50.0);
+
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(alias, false);
+
+ for (CellDesignerAnchor anchor : CellDesignerAnchor.values()) {
+ Point2D point = converter.getPointCoordinates(alias, anchor);
+ CellDesignerAnchor newAnchor = converter.getAnchorForCoordinates(alias, point);
+ assertEquals(anchor, newAnchor);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAngleConversion() {
+ Complex protein = new Complex("id");
+ protein.setWidth(10);
+ protein.setHeight(60);
+ protein.setX(200);
+ protein.setY(500);
+
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(protein, false);
+
+ for (double angle = 0.0; angle < Math.PI * 2; angle += 0.1) {
+ Point2D point = converter.getResidueCoordinates(protein, angle);
+ double angle2 = converter.getAngleForPoint(protein, point);
+ assertEquals(angle, angle2, Configuration.EPSILON);
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/testFiles/reaction_coords_different.xml b/converter-CellDesigner/testFiles/reaction_coords_different.xml
new file mode 100644
index 0000000000000000000000000000000000000000..358b5523195090382282478a588a6bd3df32d783
--- /dev/null
+++ b/converter-CellDesigner/testFiles/reaction_coords_different.xml
@@ -0,0 +1,738 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="Dopamine_Neurotransmitter_Release_Cycle" id="A_comprehensive_Parkinsons_disease_map">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>For information on content, functionalities and referencing the Parkinson's disease map, click <a target="_blank" href="http://pdmap.uni.lu">here</a>.
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
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+</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+CDK5 signaling
+</celldesigner:layerNotes>
+<celldesigner:bounds x="13264.166666666666" y="801.0" w="1493.0" h="594.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+Cell death
+</celldesigner:layerNotes>
+<celldesigner:bounds x="7350.0" y="7820.0" w="892.0" h="1064.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+Mitochondrial fusion and fission
+</celldesigner:layerNotes>
+<celldesigner:bounds x="8260.0" y="8007.0" w="2945.0" h="872.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+Mitochondrial unfolded protein response
+</celldesigner:layerNotes>
+<celldesigner:bounds x="9749.0" y="7040.0" w="1146.0" h="762.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+Mitochondrial Derived Vesicles pathway
+</celldesigner:layerNotes>
+<celldesigner:bounds x="11223.0" y="7174.0" w="1096.0" h="1776.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+Mitochondrial protein translation
+</celldesigner:layerNotes>
+<celldesigner:bounds x="11814.0" y="5990.0" w="958.0" h="596.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+Chaperone-mediated autophagy
+</celldesigner:layerNotes>
+<celldesigner:bounds x="17189.0" y="6150.0" w="1569.0" h="1413.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+Lewy-body formation
+</celldesigner:layerNotes>
+<celldesigner:bounds x="18767.0" y="6216.0" w="1213.0" h="1209.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+Vesicle dynamics
+</celldesigner:layerNotes>
+<celldesigner:bounds x="17898.0" y="7567.0" w="2458.0" h="1103.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+Actin filament organization
+</celldesigner:layerNotes>
+<celldesigner:bounds x="16003.0" y="802.0" w="2037.0" h="1102.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+PPARGC1A activity
+</celldesigner:layerNotes>
+<celldesigner:bounds x="7117.0" y="2830.0" w="1174.0" h="966.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+Metal ion homeostasis
+</celldesigner:layerNotes>
+<celldesigner:bounds x="19927.0" y="8716.0" w="1049.0" h="603.0"/>
+<celldesigner:paint color="ff000000"/>
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+</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+ER stress signaling
+</celldesigner:layerNotes>
+<celldesigner:bounds x="9354.833333333332" y="2622.0" w="1333.0" h="864.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+TFEB activity
+</celldesigner:layerNotes>
+<celldesigner:bounds x="11998.833333333332" y="2622.0" w="744.0" h="1059.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+Projection areas
+</celldesigner:layerNotes>
+<celldesigner:bounds x="25656.0" y="4540.0" w="1632.0" h="4442.0"/>
+<celldesigner:paint color="ff000000"/>
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+</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+Striatal D1 neuron intracellular signaling
+</celldesigner:layerNotes>
+<celldesigner:bounds x="23105.0" y="5201.0" w="1533.0" h="1546.0"/>
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+</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
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+Striatal D2 neuron intracellular signaling
+</celldesigner:layerNotes>
+<celldesigner:bounds x="22995.0" y="7864.0" w="1345.0" h="755.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+</celldesigner:listOfTexts>
+</celldesigner:layer>
+</celldesigner:listOfLayers>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT06704" kind="mole"/>
+</listOfUnits>
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+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
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+</listOfUnits>
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+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT06706" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
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+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s12603" id="s12603" name="PTPN5" compartment="default" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr229</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s12631" id="s12631" name="ERK1/2" compartment="default" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>ERK1/2</celldesigner:name>
+</celldesigner:speciesIdentity>
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+</rdf:RDF>
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+<reaction metaid="re5868" id="re5868" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>NEGATIVE_INFLUENCE</celldesigner:reactionType>
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+<celldesigner:linkAnchor position="E"/>
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+</celldesigner:baseReactants>
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+<annotation>
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+<celldesigner:alias>sa11783</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT06470" species="s12631">
+<annotation>
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diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
index 8ac01b531517e7c20733570abf3ce46146d8abb5..b2ac57a7e553a6786ed8a11931fe380a511c1b82 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
@@ -46,13 +46,13 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
* scale} parameters. Scale defines magnification of the image (it's a double
* value), whereas level defines how far from the top we are in hierarchical
* view (it's an integer usually in the range <0..7>. Usually there is
- * corellation between scale and level, but it's not obligatory. Level=0 means
+ * correlation between scale and level, but it's not obligatory. Level=0 means
* that we want to see as little elements as possible, whereas level=infinity
* means that we want to see everything</li>
* </ul>
*
* <p>
- * All draw operations are performed in default constractor. Therefore if we
+ * All draw operations are performed in default constructor. Therefore if we
* want to create image of a different part of the map we have to create new
* object. There are few reasons of that:
* <ul>
@@ -69,1094 +69,1082 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
*/
public abstract class AbstractImageGenerator {
- /**
- * Class that allows to check if element is visible (or transparent) when
- * drawing. It's used to filter out invisible elements when drawing
- * semantic/hierarchy view.
- */
- private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
-
- /**
- * Model is drawn as a partial image (x,y,width,height parameters of
- * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
- * Params} class. This partial image sometimes contains some object that
- * doesn't intersect with this border (usually text descriptions). This margin
- * defines how far extend drawing.
- *
- * TODO maybe more effecient (and safe) solution would be to include text
- * desciption as parts of the object border
- */
- private static final int SINGLE_FRAME_MARGIN = 100;
-
- /**
- * On which level in hierarchical view we should visualize map.
- */
- private int level = Integer.MAX_VALUE;
-
- /**
- * Zoom factor of the drawing.
- */
- private double scale = 1;
-
- /**
- * This is a frame border from which we take all elements to draw.
- */
- private Rectangle2D.Double border = null;
-
- /**
- * Object that helps to convert {@link ColorSchema} values into colors.
- */
- private ColorExtractor colorExtractor = null;
-
- /**
- * Util class for simple operations on {@link Element elements}.
- */
- private ElementUtils eu = new ElementUtils();
-
- /**
- * This class contains a list of params that are used for drawing.
- *
- * @author Piotr Gawron
- *
- */
- public static class Params {
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(Params.class);
-
- /**
- * Scale at which we want to visualize the map. The default value is 1.0 (no
- * magnification).
- */
- private double scale = 1;
-
- /**
- * x coordinate from which we start to draw a map. This is absolute value on
- * the map (scale doesn't influence it).
- */
-
- private double x = 0;
-
- /**
- * y coordinate from which we start to draw a map. This is absolute value on
- * the map (scale doesn't influence it).
- */
- private double y = 0;
-
- /**
- * width of the generated image. It's an absolute value in pixels, therefore
- * when scale is set to value different than 1.0 the width on the map will
- * also be modified to fit into width pixels.
- */
- private Double width = null;
-
- /**
- * height of the generated image. It's an absolute value in pixels,
- * therefore when scale is set to value different than 1.0 the height on the
- * map will also be modified to fit into height pixels.
- */
- private Double height = null;
-
- /**
- * Model to be visualized.
- */
- private Model model = null;
-
- /**
- * Should we draw white background.
- */
- private boolean background = true;
-
- /**
- * At which hierarchy level we visualize map. Level=0 means that we want to
- * see as little elements as possible, whereas level=infinity means that we
- * want to see everything.
- */
- private int level = Integer.MAX_VALUE;
-
- /**
- * Should the visualization include hierarchical view or not.
- */
- private boolean nested = false;
-
- /**
- * Should sbgn standard be used.
- */
- private boolean sbgn = false;
-
- /**
- * List of objects containging information about layouts visualized in the
- * javascript (on client side). Every object (map) represents data for
- * single layout. In this map we have pairs between {@link Element}/
- * {@link Reaction} and {@link ColorSchema} used to visualize the element.
- *
- */
- private List<Map<Object, ColorSchema>> visibleLayouts = new ArrayList<>();
-
- /**
- * Color that should be used for drawing overlays with minimum value.
- */
- private Color minColor = Color.BLACK;
-
- /**
- * Color that should be used for drawing overlays with maximum value.
- */
- private Color maxColor = Color.BLACK;
-
- private Color simpleColor = Color.BLACK;
-
- /**
- * @param scale
- * scale to set
- * @return object with all parameters
- * @see #scale
- */
- public Params scale(final double scale) {
- this.scale = scale;
- return this;
- }
-
- /**
- * @param scale
- * scale to set
- * @return object with all parameters
- * @see #scale
- */
- public Params scale(final int scale) {
- this.scale = scale;
- return this;
- }
-
- /**
- *
- * @param x
- * x coordinate to be set
- * @return object with all parameters
- * @see #x
- */
- public Params x(final double x) {
- this.x = x;
- return this;
- }
-
- /**
- * @param x
- * x coordinate to be set
- * @return object with all parameters
- * @see #x
- */
- public Params x(final int x) {
- this.x = x;
- return this;
- }
-
- /**
- * @param y
- * y coordinate to be set
- * @return object with all parameters
- * @see #y
- */
- public Params y(final double y) {
- this.y = y;
- return this;
- }
-
- /**
- * @param y
- * y coordinate to be set
- * @return object with all parameters
- * @see #y
- */
- public Params y(final int y) {
- this.y = y;
- return this;
- }
-
- /**
- * @param width
- * width to set
- * @return object with all parameters
- * @see #width
- */
- public Params width(final double width) {
- this.width = width;
- return this;
- }
-
- /**
- * @param width
- * width to set
- * @return object with all parameters
- * @see #width
- */
- public Params width(final int width) {
- this.width = (double) width;
- return this;
- }
-
- /**
- *
- * @param height
- * height to set
- * @return object with all parameters
- * @see #height
- */
- public Params height(final double height) {
- this.height = height;
- return this;
- }
-
- /**
- * @param height
- * height to set
- * @return object with all parameters
- * @see #height
- */
- public Params height(final int height) {
- this.height = (double) height;
- return this;
- }
-
- /**
- *
- * @param background
- * background flag to set
- * @return object with all parameters
- * @see #background
- */
- public Params background(final boolean background) {
- this.background = background;
- return this;
- }
-
- /**
- *
- * @param nested
- * nested flag to set
- * @return object with all parameters
- * @see #nested
- */
- public Params nested(final boolean nested) {
- this.nested = nested;
- return this;
- }
-
- /**
- *
- * @param model
- * model to set
- * @return object with all parameters
- * @see #model
- */
- public Params model(final Model model) {
- this.model = model;
- if (this.width == null) {
- this.width = model.getWidth();
- }
- if (this.height == null) {
- this.height = model.getHeight();
- }
- return this;
- }
-
- /**
- *
- * @param level
- * level to set
- * @return object with all parameters
- * @see #level
- */
- public Params level(final int level) {
- this.level = level;
- return this;
- }
-
- /**
- *
- * @return scale value
- * @see #scale
- */
- public double getScale() {
- return scale;
- }
-
- /**
- *
- * @return x coordinate value
- * @see #x
- */
- public double getX() {
- return x;
- }
-
- /**
- *
- * @return y coordinate value
- * @see #y
- */
- public double getY() {
- return y;
- }
-
- /**
- *
- * @return width value
- * @see #width
- */
- public double getWidth() {
- return width;
- }
-
- /**
- *
- * @return height value
- * @see #height
- */
- public double getHeight() {
- return height;
- }
-
- /**
- *
- * @return model object
- * @see #model
- */
- public Model getModel() {
- return model;
- }
-
- /**
- *
- * @return background value
- * @see #background
- */
- public boolean isBackground() {
- return background;
- }
-
- /**
- *
- * @return nested value
- * @see #nested
- */
- public boolean isNested() {
- return nested;
- }
-
- /**
- * @return the level
- * @see #level
- */
- public int getLevel() {
- return level;
- }
-
- /**
- * Sets {@link #level} parameter from {@link String}.
- *
- * @param zoomLevel
- * new {@link #level} value
- * @return object with all parameters
- */
- public Params level(String zoomLevel) {
- if (zoomLevel == null) {
- logger.warn("Parameter equals to null...");
- } else {
- this.level = Integer.valueOf(zoomLevel);
- }
- return this;
- }
-
- @Override
- public String toString() {
- String result = "[" + this.getClass().getSimpleName() + "] " + "Model:" + model + "," +
- "scale:" + scale + "," +
- "x:" + x + "," +
- "y:" + y + "," +
- "width:" + width + "," +
- "height:" + height + "," +
- "background:" + background + "," +
- "level:" + level + "," +
- "nested:" + nested + ",";
- return result;
- }
-
- /**
- * Adds layout data that is visualized on the client side. Layout data
- * contains mapping between {@link Element}/{@link Reaction} and
- * {@link ColorSchema} used for coloring specific element.
- *
- * @param map
- * layout data containing mapping between {@link Element}/
- * {@link Reaction} and {@link ColorSchema} used for coloring
- * specific element
- */
- public void addVisibleLayout(Map<Object, ColorSchema> map) {
- visibleLayouts.add(map);
- }
-
- /**
- * @return the visibleLayouts
- * @see #visibleLayouts
- */
- public List<Map<Object, ColorSchema>> getVisibleLayouts() {
- return visibleLayouts;
- }
-
- /**
- * Returns list with {@link ColorSchema} used to visualize the specific
- * object in layouts visualized in the javascript.
- *
- * @param object
- * object ({@link Element} or {@link Reaction}) for which we return
- * list of {@link ColorSchema} in different layouts
- * @return list with {@link ColorSchema} used to visualize the specific
- * object in layouts visualized in the javascript
- * @see #visibleLayouts
- */
- public List<ColorSchema> getVisibleLayoutsForElement(Object object) {
- List<ColorSchema> result = new ArrayList<>();
- for (Map<Object, ColorSchema> map : visibleLayouts) {
- result.add(map.get(object));
- }
- return result;
- }
-
- /**
- * Returns {@link Color} that should be used for drawing overlays with
- * maximum value.
- *
- * @return {@link Color} that should be used for drawing overlays with
- * maximum value
- */
- public Color getMaxColor() {
- return maxColor;
- }
-
- public Color getSimpleColor() {
- return simpleColor;
- }
-
- /**
- * Returns {@link Color} that should be used for drawing overlays with
- * minimum value.
- *
- * @return {@link Color} that should be used for drawing overlays with
- * minimum value
- */
- public Color getMinColor() {
- return minColor;
- }
-
- /**
- * @param minColor
- * minColor to set
- * @return object with all parameters
- * @see #minColor
- */
- public Params minColor(Color minColor) {
- this.minColor = minColor;
- return this;
- }
-
- /**
- * @param maxColor
- * maxColor to set
- * @return object with all parameters
- * @see #maxColor
- */
- public Params maxColor(Color maxColor) {
- this.maxColor = maxColor;
- return this;
- }
-
- /**
- * @param simpleColor
- * simpleColor to set
- * @return object with all parameters
- * @see #simpleColor
- */
- public Params simpleColor(Color simpleColor) {
- this.simpleColor = simpleColor;
- return this;
- }
-
- /**
- * @return the sbgn
- * @see #sbgn
- */
- public boolean isSbgn() {
- return sbgn;
- }
-
- /**
- * @param sbgn
- * the sbgn to set
- * @see #sbgn
- * @return object with all parameters
- */
- public Params sbgn(boolean sbgn) {
- this.sbgn = sbgn;
- return this;
- }
-
- public Params colorExtractor(ColorExtractor colorExtractor) {
- return minColor(colorExtractor.getMinColor()).
- maxColor(colorExtractor.getMaxColor()).
- simpleColor(colorExtractor.getSimpleColor());
- }
-
- }
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(AbstractImageGenerator.class);
-
- /**
- * Graphics object which allows to draw objects.
- */
- private Graphics2D graphics;
-
- /**
- * SBGN display format.
- */
- private boolean sbgnFormat = false;
-
- /**
- * List of params used for drawing.
- */
- private Params params;
-
- /**
- * This method creates a graphics object for different implementations of
- * canvas with fixed width and height.
- *
- * @param width
- * width of the canvas (graphics2d) to be created
- * @param height
- * height of the canvas (graphics2d) to be created
- */
- protected abstract void createImageObject(double width, double height);
-
- /**
- * Default constructor. Create an image that is described by params. For more
- * information see
- * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
- * params}.
- *
- * @param params
- * list of all params to create apropriate image
- * @throws DrawingException
- * thrown when there was a problem with drawing a map
- *
- */
- protected AbstractImageGenerator(final Params params) {
- this.params = params;
- }
-
- /**
- * Flag indicating {@link #draw()} method was executed.
- */
- private boolean drawn = false;
-
- /**
- * Draw a model into {@link #getGraphics()} object.
- *
- * @throws DrawingException
- * thrown when there is a problem with drawing
- */
- protected void draw() throws DrawingException {
- if (isDrawn()) {
- logger.warn("Model was already drawn. Skipping");
- return;
- }
- this.level = params.getLevel();
- this.scale = params.getScale();
-
- colorExtractor = new ColorExtractor(params.getMinColor(), params.getMaxColor(), params.getSimpleColor());
-
- // set border frame extended by a margin
- border = new Rectangle2D.Double(
- params.getX() - SINGLE_FRAME_MARGIN, params.getY() - SINGLE_FRAME_MARGIN, params.getWidth() * scale + 2 * SINGLE_FRAME_MARGIN,
- params.getHeight() * scale + 2 * SINGLE_FRAME_MARGIN);
- createImageObject(params.getWidth(), params.getHeight());
-
- // turn on anti-aliasing
- graphics.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
-
- graphics.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
-
- graphics.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY);
-
- // set scale
- graphics.scale(1 / scale, 1 / scale);
-
- // move the upper left corner to coordinates
- graphics.translate(-params.getX(), -params.getY());
-
- if (params.isBackground()) {
- // create a background
- graphics.setColor(Color.WHITE);
- graphics.fillRect(
- (int) params.getX() - 1, (int) params.getY() - 1, ((int) Math.ceil(params.getWidth() * scale)) + 2,
- ((int) Math.ceil(params.getHeight() * scale)) + 2);
- graphics.setColor(Color.BLACK);
- }
-
- // Get the SBGN display format option from the model
- this.sbgnFormat = params.isSbgn();
-
- // Correct order of displaying is: elements, reactions, compartments,
- // layers.
- // In this way we can display all reactions and overlay them by compartments
- // or layers if they should be solid and hide complexity behind it
-
- // draw all elements
- for (Element element : params.getModel().getSortedSpeciesList()) {
- // draw only elements that don't have parents (aren't included in any
- // compartment/complexes)
- if (element instanceof Species) {
- if (((Species) element).getComplex() == null && element.getCompartment() == null) {
- drawSpecies((Species) element);
- }
- }
- }
- // draw all reactions
- for (Reaction reaction : params.getModel().getSortedReactions()) {
- drawReaction(reaction);
- }
- // draw all compartments
- for (Compartment compartment : params.getModel().getSortedCompartments()) {
- // draw only compartment that don't have parents (aren't included in any
- // compartment/complexes)
- if (compartment.getCompartment() == null) {
- drawCompartment(compartment);
- }
- }
-
- // draw all layers
- for (Layer layer : params.getModel().getLayers()) {
- drawLayer(layer);
- }
- closeImageObject();
- setDrawn(true);
- }
-
- /**
- * Method called after drawing. It should close drawing canvas properly.
- */
- protected abstract void closeImageObject();
-
- /**
- * This method draw layer on the graphics.
- *
- * @param layer
- * layer to be drawn
- */
- private void drawLayer(final Layer layer) {
- // get a converter nad set text borders to no
- LayerConverter converter = new LayerConverter(false);
- converter.drawLayer(layer, graphics);
- }
-
- /**
- * Don't allow to create default public constructors with empty list of
- * parameters.
- */
- protected AbstractImageGenerator() {
- super();
- }
-
- /**
- * This method draw a {@link Compartment} on a graphics.
- *
- * @param compartment
- * object that we want to draw
- * @throws DrawingException
- * thrown when there was a problem with drawing {@link Compartment}
- */
- protected void drawCompartment(final Compartment compartment) throws DrawingException {
- // get a converter for this compartment
- BioEntityConverterImpl converter = new BioEntityConverterImpl(compartment, colorExtractor);
- ConverterParams compartmentParams = new ConverterParams().level(level).nested(params.nested);
-
- if (params.nested) {
- compartmentParams.scale(Math.max(scale, 1));
- }
-
- // we draw compartment only when we have hierarchical view or it's
- // standard compartment (not the pathway)
- if (params.nested || !(compartment instanceof PathwayCompartment)) {
- converter.draw(compartment, graphics, compartmentParams, params.getVisibleLayoutsForElement(compartment));
- }
-
- // If compartment should be filled, then we could skip drawing the inside
- // compartments.
-
- if (zoomLevelMatcher.isTransparent(level, compartment.getTransparencyLevel()) || !params.nested) {
- List<Element> result = new ArrayList<>();
- result.addAll(compartment.getElements());
- Collections.sort(result, Element.SIZE_COMPARATOR);
-
- // draw all children of this compartment
- for (Element child : result) {
- // if a child is a standard species
- if (child instanceof Species) {
- drawSpecies((Species) child);
- } else if (child instanceof Compartment) {
- drawCompartment((Compartment) child);
- } else {
- // if a child is not a compartment or a species then we have a
- // problem
- throw new DrawingException(eu.getElementTag(child) + "Unknown Element type");
- }
-
- }
- if (!compartment.containsIdenticalSpecies()) {
- if (!(compartment instanceof PathwayCompartment)) {
- converter.drawText(compartment, graphics, compartmentParams);
- }
- }
- }
- }
-
- /**
- * This method draw a {@link Species} on a graphics.
- *
- * @param species
- * object to be drawn
- * @throws DrawingException
- * thrown when there was a problem with drawing a {@link Species}
- */
- protected void drawSpecies(final Species species) throws DrawingException {
- if (!cross(species.getBorder())) {
- return;
- }
-
- boolean rescale = false;
- if (species instanceof Complex) {
- Complex complex = (Complex) species;
- if (complex.getElements().size() == 0) {
- rescale = true;
- } else {
- rescale = true;
- for (Element child : complex.getElements()) {
- if ((zoomLevelMatcher.isVisible(level, child.getVisibilityLevel())) || !params.nested) {
- rescale = false;
- }
- }
- }
- }
-
- // at the beginning try to find an appropriate converter
- BioEntityConverterImpl converter = new BioEntityConverterImpl(species, sbgnFormat, colorExtractor);
- double customScale = 1;
- if (rescale) {
- customScale = scale;
- }
- converter.draw(
- species, graphics, new ConverterParams().scale(customScale).level(level).sbgnFormat(sbgnFormat).nested(params.nested),
- params.getVisibleLayoutsForElement(species));
-
- // if the species is a complex then we may want to draw children
- // objects
- if (species instanceof Complex) {
- Complex complex = (Complex) species;
- // before drawing children check if the view is not set to brief
- // mode
- if (!complex.getState().equalsIgnoreCase("brief")) {
- // depending on current zoom level, children are drawn or not
- if (zoomLevelMatcher.isTransparent(level, complex.getTransparencyLevel()) || !params.nested) {
- for (Species child : complex.getElements()) {
- drawSpecies(child);
- }
- }
- }
- }
- }
-
- /**
- * This method draw a reaction on a graphics.
- *
- * @param reaction
- * object to be drawn
- * @throws DrawingException
- * thrown when there was a problem with drawing a {@link Reaction}
- */
- protected void drawReaction(final Reaction reaction) throws DrawingException {
- if (!cross(reaction.getLines())) {
- return;
- }
- BioEntityConverterImpl converter = new BioEntityConverterImpl(reaction, sbgnFormat, colorExtractor);
- converter.draw(
- reaction, graphics, new ConverterParams().sbgnFormat(sbgnFormat).nested(params.nested).level(level), params.getVisibleLayoutsForElement(reaction));
- }
-
- /**
- * Checks if one of the lines in parameter cross the frame.
- *
- * @param lines
- * list of lines to check
- * @return true if the cross point exist, false otherwise
- */
- private boolean cross(final List<Line2D> lines) {
- for (Line2D line2d : lines) {
- if (border.intersectsLine(line2d)) {
- return true;
- }
- }
- return false;
- }
-
- /**
- * Checks if the rectangle in the parameters cross the fram in which we are
- * currently draw image.
- *
- * @param rect
- * rectangle to check
- * @return true if rectangle check the frame, false otherwise
- */
- protected boolean cross(final Rectangle2D rect) {
- return border.intersects(rect);
- }
-
- /**
- * @return the graphics
- */
- protected Graphics2D getGraphics() {
- return graphics;
- }
-
- /**
- * @param graphics
- * the graphics to set
- */
- protected void setGraphics(Graphics2D graphics) {
- this.graphics = graphics;
- }
-
- /**
- * Saves generated image into file.
- *
- * @param fileName
- * file where the images should be saved
- * @throws IOException
- * thrown when there is problem with output file
- * @throws DrawingException
- * thrown when there was a problem with drawing map
- */
- public final void saveToFile(String fileName) throws IOException, DrawingException {
- if (!isDrawn()) {
- draw();
- }
- saveToFileImplementation(fileName);
- };
-
- /**
- * Saves generated image from {@link #getGraphics()} into file.
- *
- * @param fileName
- * file where the images should be saved
- * @throws IOException
- * thrown when there is problem with output file
- * @throws DrawingException
- * thrown when there was a problem with drawing map
- */
- protected abstract void saveToFileImplementation(String fileName) throws IOException;
-
- /**
- * Saves generated image into {@link OutputStream}.
- *
- * @param os
- * stream where the images should be saved
- * @throws IOException
- * thrown when there is problem with output stream
- * @throws DrawingException
- * thrown when there was a problem with drawing map
- */
- public final void saveToOutputStream(OutputStream os) throws IOException, DrawingException {
- if (!isDrawn()) {
- draw();
- }
- saveToOutputStreamImplementation(os);
- }
-
- /**
- * Saves generated image from {@link #getGraphics()} into {@link OutputStream}
- * .
- *
- * @param os
- * stream where the images should be saved
- * @throws IOException
- * thrown when there is problem with output stream
- * @throws DrawingException
- * thrown when there was a problem with drawing map
- */
- protected abstract void saveToOutputStreamImplementation(OutputStream os) throws IOException;
-
- /**
- * Saves part of the generated image file.
- *
- * @param fileName
- * file where the images should be saved
- * @param x
- * x left margin of the image part
- * @param y
- * y top margin of the image part
- * @param width
- * width of the image part
- * @param height
- * hieght of the image part
- * @throws IOException
- * thrown when there is problem with output file
- * @throws DrawingException
- * thrown when there was a problem with drawing map
- */
- public final void savePartToFile(final int x, final int y, final int width, final int height, final String fileName) throws IOException, DrawingException {
- if (!isDrawn()) {
- draw();
- }
- savePartToFileImplementation(x, y, width, height, fileName);
- }
-
- /**
- * Saves part of the generated image from {@link #getGraphics()} into file.
- *
- * @param fileName
- * file where the images should be saved
- * @param x
- * x left margin of the image part
- * @param y
- * y top margin of the image part
- * @param width
- * width of the image part
- * @param height
- * hieght of the image part
- * @throws IOException
- * thrown when there is problem with output file
- */
- protected abstract void savePartToFileImplementation(final int x, final int y, final int width, final int height, final String fileName) throws IOException;
-
- /**
- * Saves part of the generated image into {@link OutputStream}.
- *
- * @param os
- * stream where the images should be saved
- * @param x
- * x left margin of the image part
- * @param y
- * y top margin of the image part
- * @param width
- * width of the image part
- * @param height
- * hieght of the image part
- * @throws IOException
- * thrown when there is problem with output file
- * @throws DrawingException
- * thrown when there was a problem with drawing map
- */
- public final void savePartToOutputStream(final int x, final int y, final int width, final int height, final OutputStream os)
- throws IOException, DrawingException {
- if (!isDrawn()) {
- draw();
- }
- savePartToOutputStreamImplementation(x, y, width, height, os);
- }
-
- /**
- * Saves part of the generated image from {@link #getGraphics()} into
- * {@link OutputStream}.
- *
- * @param os
- * stream where the images should be saved
- * @param x
- * x left margin of the image part
- * @param y
- * y top margin of the image part
- * @param width
- * width of the image part
- * @param height
- * hieght of the image part
- * @throws IOException
- * thrown when there is problem with output file
- * @throws DrawingException
- * thrown when there was a problem with drawing map
- */
- protected abstract void savePartToOutputStreamImplementation(final int x, final int y, final int width, final int height, final OutputStream os)
- throws IOException;
-
- /**
- * Returns name of the format to which this graphic converter will transform.
- *
- * @return name of the format to which this graphic converter will transform
- */
- public abstract String getFormatName();
-
- /**
- * Returns {@link MimeType} that should be used for files generated by this
- * image generator.
- *
- * @return {@link MimeType} that should be used for files generated by this
- * image generator
- */
- public abstract MimeType getMimeType();
-
- /**
- * Returns default file extension used by this image generator.
- *
- * @return default file extension used by this image generator
- */
- public abstract String getFileExtension();
-
- /**
- * @return the sbgnFormat
- */
- protected boolean isSbgnFormat() {
- return sbgnFormat;
- }
-
- /**
- * @param sbgnFormat
- * the sbgnFormat to set
- */
- protected void sbgnFormat(boolean sbgnFormat) {
- this.sbgnFormat = sbgnFormat;
- }
-
- /**
- * @return the drawn
- * @see #drawn
- */
- private boolean isDrawn() {
- return drawn;
- }
-
- /**
- * @param drawn
- * the drawn to set
- * @see #drawn
- */
- private void setDrawn(boolean drawn) {
- this.drawn = drawn;
- }
-
- /**
- * @return the params
- * @see #params
- */
- protected Params getParams() {
- return params;
- }
-
- /**
- * @param params
- * the params to set
- * @see #params
- */
- protected void setParams(Params params) {
- this.params = params;
- }
+ /**
+ * Class that allows to check if element is visible (or transparent) when
+ * drawing. It's used to filter out invisible elements when drawing
+ * semantic/hierarchy view.
+ */
+ private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
+
+ /**
+ * Model is drawn as a partial image (x,y,width,height parameters of
+ * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
+ * Params} class. This partial image sometimes contains some object that doesn't
+ * intersect with this border (usually text descriptions). This margin defines
+ * how far extend drawing.
+ *
+ * TODO maybe more efficient (and safe) solution would be to include text
+ * Description as parts of the object border
+ */
+ private static final int SINGLE_FRAME_MARGIN = 100;
+
+ /**
+ * On which level in hierarchical view we should visualize map.
+ */
+ private int level = Integer.MAX_VALUE;
+
+ /**
+ * Zoom factor of the drawing.
+ */
+ private double scale = 1;
+
+ /**
+ * This is a frame border from which we take all elements to draw.
+ */
+ private Rectangle2D.Double border = null;
+
+ /**
+ * Object that helps to convert {@link ColorSchema} values into colors.
+ */
+ private ColorExtractor colorExtractor = null;
+
+ /**
+ * Util class for simple operations on {@link Element elements}.
+ */
+ private ElementUtils eu = new ElementUtils();
+
+ /**
+ * This class contains a list of params that are used for drawing.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ public static class Params {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(Params.class);
+
+ /**
+ * Scale at which we want to visualize the map. The default value is 1.0 (no
+ * magnification).
+ */
+ private double scale = 1;
+
+ /**
+ * x coordinate from which we start to draw a map. This is absolute value on the
+ * map (scale doesn't influence it).
+ */
+
+ private double x = 0;
+
+ /**
+ * y coordinate from which we start to draw a map. This is absolute value on the
+ * map (scale doesn't influence it).
+ */
+ private double y = 0;
+
+ /**
+ * width of the generated image. It's an absolute value in pixels, therefore
+ * when scale is set to value different than 1.0 the width on the map will also
+ * be modified to fit into width pixels.
+ */
+ private Double width = null;
+
+ /**
+ * height of the generated image. It's an absolute value in pixels, therefore
+ * when scale is set to value different than 1.0 the height on the map will also
+ * be modified to fit into height pixels.
+ */
+ private Double height = null;
+
+ /**
+ * Model to be visualized.
+ */
+ private Model model = null;
+
+ /**
+ * Should we draw white background.
+ */
+ private boolean background = true;
+
+ /**
+ * At which hierarchy level we visualize map. Level=0 means that we want to see
+ * as little elements as possible, whereas level=infinity means that we want to
+ * see everything.
+ */
+ private int level = Integer.MAX_VALUE;
+
+ /**
+ * Should the visualization include hierarchical view or not.
+ */
+ private boolean nested = false;
+
+ /**
+ * Should sbgn standard be used.
+ */
+ private boolean sbgn = false;
+
+ /**
+ * List of objects containging information about layouts visualized in the
+ * javascript (on client side). Every object (map) represents data for single
+ * layout. In this map we have pairs between {@link Element}/ {@link Reaction}
+ * and {@link ColorSchema} used to visualize the element.
+ *
+ */
+ private List<Map<Object, ColorSchema>> visibleLayouts = new ArrayList<>();
+
+ /**
+ * Color that should be used for drawing overlays with minimum value.
+ */
+ private Color minColor = Color.BLACK;
+
+ /**
+ * Color that should be used for drawing overlays with maximum value.
+ */
+ private Color maxColor = Color.BLACK;
+
+ private Color simpleColor = Color.BLACK;
+
+ /**
+ * @param scale
+ * scale to set
+ * @return object with all parameters
+ * @see #scale
+ */
+ public Params scale(final double scale) {
+ this.scale = scale;
+ return this;
+ }
+
+ /**
+ * @param scale
+ * scale to set
+ * @return object with all parameters
+ * @see #scale
+ */
+ public Params scale(final int scale) {
+ this.scale = scale;
+ return this;
+ }
+
+ /**
+ *
+ * @param x
+ * x coordinate to be set
+ * @return object with all parameters
+ * @see #x
+ */
+ public Params x(final double x) {
+ this.x = x;
+ return this;
+ }
+
+ /**
+ * @param x
+ * x coordinate to be set
+ * @return object with all parameters
+ * @see #x
+ */
+ public Params x(final int x) {
+ this.x = x;
+ return this;
+ }
+
+ /**
+ * @param y
+ * y coordinate to be set
+ * @return object with all parameters
+ * @see #y
+ */
+ public Params y(final double y) {
+ this.y = y;
+ return this;
+ }
+
+ /**
+ * @param y
+ * y coordinate to be set
+ * @return object with all parameters
+ * @see #y
+ */
+ public Params y(final int y) {
+ this.y = y;
+ return this;
+ }
+
+ /**
+ * @param width
+ * width to set
+ * @return object with all parameters
+ * @see #width
+ */
+ public Params width(final double width) {
+ this.width = width;
+ return this;
+ }
+
+ /**
+ * @param width
+ * width to set
+ * @return object with all parameters
+ * @see #width
+ */
+ public Params width(final int width) {
+ this.width = (double) width;
+ return this;
+ }
+
+ /**
+ *
+ * @param height
+ * height to set
+ * @return object with all parameters
+ * @see #height
+ */
+ public Params height(final double height) {
+ this.height = height;
+ return this;
+ }
+
+ /**
+ * @param height
+ * height to set
+ * @return object with all parameters
+ * @see #height
+ */
+ public Params height(final int height) {
+ this.height = (double) height;
+ return this;
+ }
+
+ /**
+ *
+ * @param background
+ * background flag to set
+ * @return object with all parameters
+ * @see #background
+ */
+ public Params background(final boolean background) {
+ this.background = background;
+ return this;
+ }
+
+ /**
+ *
+ * @param nested
+ * nested flag to set
+ * @return object with all parameters
+ * @see #nested
+ */
+ public Params nested(final boolean nested) {
+ this.nested = nested;
+ return this;
+ }
+
+ /**
+ *
+ * @param model
+ * model to set
+ * @return object with all parameters
+ * @see #model
+ */
+ public Params model(final Model model) {
+ this.model = model;
+ if (this.width == null) {
+ this.width = model.getWidth();
+ }
+ if (this.height == null) {
+ this.height = model.getHeight();
+ }
+ return this;
+ }
+
+ /**
+ *
+ * @param level
+ * level to set
+ * @return object with all parameters
+ * @see #level
+ */
+ public Params level(final int level) {
+ this.level = level;
+ return this;
+ }
+
+ /**
+ *
+ * @return scale value
+ * @see #scale
+ */
+ public double getScale() {
+ return scale;
+ }
+
+ /**
+ *
+ * @return x coordinate value
+ * @see #x
+ */
+ public double getX() {
+ return x;
+ }
+
+ /**
+ *
+ * @return y coordinate value
+ * @see #y
+ */
+ public double getY() {
+ return y;
+ }
+
+ /**
+ *
+ * @return width value
+ * @see #width
+ */
+ public double getWidth() {
+ return width;
+ }
+
+ /**
+ *
+ * @return height value
+ * @see #height
+ */
+ public double getHeight() {
+ return height;
+ }
+
+ /**
+ *
+ * @return model object
+ * @see #model
+ */
+ public Model getModel() {
+ return model;
+ }
+
+ /**
+ *
+ * @return background value
+ * @see #background
+ */
+ public boolean isBackground() {
+ return background;
+ }
+
+ /**
+ *
+ * @return nested value
+ * @see #nested
+ */
+ public boolean isNested() {
+ return nested;
+ }
+
+ /**
+ * @return the level
+ * @see #level
+ */
+ public int getLevel() {
+ return level;
+ }
+
+ /**
+ * Sets {@link #level} parameter from {@link String}.
+ *
+ * @param zoomLevel
+ * new {@link #level} value
+ * @return object with all parameters
+ */
+ public Params level(String zoomLevel) {
+ if (zoomLevel == null) {
+ logger.warn("Parameter equals to null...");
+ } else {
+ this.level = Integer.valueOf(zoomLevel);
+ }
+ return this;
+ }
+
+ @Override
+ public String toString() {
+ String result = "[" + this.getClass().getSimpleName() + "] " + "Model:" + model + "," + "scale:" + scale + ","
+ + "x:" + x + "," + "y:" + y + "," + "width:" + width + "," + "height:" + height + "," + "background:"
+ + background + "," + "level:" + level + "," + "nested:" + nested + ",";
+ return result;
+ }
+
+ /**
+ * Adds layout data that is visualized on the client side. Layout data contains
+ * mapping between {@link Element}/{@link Reaction} and {@link ColorSchema} used
+ * for coloring specific element.
+ *
+ * @param map
+ * layout data containing mapping between {@link Element}/
+ * {@link Reaction} and {@link ColorSchema} used for coloring specific
+ * element
+ */
+ public void addVisibleLayout(Map<Object, ColorSchema> map) {
+ visibleLayouts.add(map);
+ }
+
+ /**
+ * @return the visibleLayouts
+ * @see #visibleLayouts
+ */
+ public List<Map<Object, ColorSchema>> getVisibleLayouts() {
+ return visibleLayouts;
+ }
+
+ /**
+ * Returns list with {@link ColorSchema} used to visualize the specific object
+ * in layouts visualized in the javascript.
+ *
+ * @param object
+ * object ({@link Element} or {@link Reaction}) for which we return
+ * list of {@link ColorSchema} in different layouts
+ * @return list with {@link ColorSchema} used to visualize the specific object
+ * in layouts visualized in the javascript
+ * @see #visibleLayouts
+ */
+ public List<ColorSchema> getVisibleLayoutsForElement(Object object) {
+ List<ColorSchema> result = new ArrayList<>();
+ for (Map<Object, ColorSchema> map : visibleLayouts) {
+ result.add(map.get(object));
+ }
+ return result;
+ }
+
+ /**
+ * Returns {@link Color} that should be used for drawing overlays with maximum
+ * value.
+ *
+ * @return {@link Color} that should be used for drawing overlays with maximum
+ * value
+ */
+ public Color getMaxColor() {
+ return maxColor;
+ }
+
+ public Color getSimpleColor() {
+ return simpleColor;
+ }
+
+ /**
+ * Returns {@link Color} that should be used for drawing overlays with minimum
+ * value.
+ *
+ * @return {@link Color} that should be used for drawing overlays with minimum
+ * value
+ */
+ public Color getMinColor() {
+ return minColor;
+ }
+
+ /**
+ * @param minColor
+ * minColor to set
+ * @return object with all parameters
+ * @see #minColor
+ */
+ public Params minColor(Color minColor) {
+ this.minColor = minColor;
+ return this;
+ }
+
+ /**
+ * @param maxColor
+ * maxColor to set
+ * @return object with all parameters
+ * @see #maxColor
+ */
+ public Params maxColor(Color maxColor) {
+ this.maxColor = maxColor;
+ return this;
+ }
+
+ /**
+ * @param simpleColor
+ * simpleColor to set
+ * @return object with all parameters
+ * @see #simpleColor
+ */
+ public Params simpleColor(Color simpleColor) {
+ this.simpleColor = simpleColor;
+ return this;
+ }
+
+ /**
+ * @return the sbgn
+ * @see #sbgn
+ */
+ public boolean isSbgn() {
+ return sbgn;
+ }
+
+ /**
+ * @param sbgn
+ * the sbgn to set
+ * @see #sbgn
+ * @return object with all parameters
+ */
+ public Params sbgn(boolean sbgn) {
+ this.sbgn = sbgn;
+ return this;
+ }
+
+ public Params colorExtractor(ColorExtractor colorExtractor) {
+ return minColor(colorExtractor.getMinColor()).maxColor(colorExtractor.getMaxColor())
+ .simpleColor(colorExtractor.getSimpleColor());
+ }
+
+ }
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(AbstractImageGenerator.class);
+
+ /**
+ * Graphics object which allows to draw objects.
+ */
+ private Graphics2D graphics;
+
+ /**
+ * SBGN display format.
+ */
+ private boolean sbgnFormat = false;
+
+ /**
+ * List of params used for drawing.
+ */
+ private Params params;
+
+ /**
+ * This method creates a graphics object for different implementations of canvas
+ * with fixed width and height.
+ *
+ * @param width
+ * width of the canvas (graphics2d) to be created
+ * @param height
+ * height of the canvas (graphics2d) to be created
+ */
+ protected abstract void createImageObject(double width, double height);
+
+ /**
+ * Default constructor. Create an image that is described by params. For more
+ * information see
+ * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
+ * params}.
+ *
+ * @param params
+ * list of all params to create apropriate image
+ * @throws DrawingException
+ * thrown when there was a problem with drawing a map
+ *
+ */
+ protected AbstractImageGenerator(final Params params) {
+ this.params = params;
+ }
+
+ /**
+ * Flag indicating {@link #draw()} method was executed.
+ */
+ private boolean drawn = false;
+
+ /**
+ * Draw a model into {@link #getGraphics()} object.
+ *
+ * @throws DrawingException
+ * thrown when there is a problem with drawing
+ */
+ protected void draw() throws DrawingException {
+ if (isDrawn()) {
+ logger.warn("Model was already drawn. Skipping");
+ return;
+ }
+ this.level = params.getLevel();
+ this.scale = params.getScale();
+
+ colorExtractor = new ColorExtractor(params.getMinColor(), params.getMaxColor(), params.getSimpleColor());
+
+ // set border frame extended by a margin
+ border = new Rectangle2D.Double(params.getX() - SINGLE_FRAME_MARGIN, params.getY() - SINGLE_FRAME_MARGIN,
+ params.getWidth() * scale + 2 * SINGLE_FRAME_MARGIN, params.getHeight() * scale + 2 * SINGLE_FRAME_MARGIN);
+ createImageObject(params.getWidth(), params.getHeight());
+
+ // turn on anti-aliasing
+ graphics.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+
+ graphics.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
+
+ graphics.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY);
+
+ // set scale
+ graphics.scale(1 / scale, 1 / scale);
+
+ // move the upper left corner to coordinates
+ graphics.translate(-params.getX(), -params.getY());
+
+ if (params.isBackground()) {
+ // create a background
+ graphics.setColor(Color.WHITE);
+ graphics.fillRect((int) params.getX() - 1, (int) params.getY() - 1,
+ ((int) Math.ceil(params.getWidth() * scale)) + 2, ((int) Math.ceil(params.getHeight() * scale)) + 2);
+ graphics.setColor(Color.BLACK);
+ }
+
+ // Get the SBGN display format option from the model
+ this.sbgnFormat = params.isSbgn();
+
+ // Correct order of displaying is: elements, reactions, compartments,
+ // layers.
+ // In this way we can display all reactions and overlay them by compartments
+ // or layers if they should be solid and hide complexity behind it
+
+ // draw all elements
+ for (Element element : params.getModel().getSortedSpeciesList()) {
+ // draw only elements that don't have parents (aren't included in any
+ // compartment/complexes)
+ if (element instanceof Species) {
+ if (((Species) element).getComplex() == null && element.getCompartment() == null) {
+ drawSpecies((Species) element);
+ }
+ }
+ }
+ // draw all reactions
+ for (Reaction reaction : params.getModel().getSortedReactions()) {
+ drawReaction(reaction);
+ }
+ // draw all compartments
+ for (Compartment compartment : params.getModel().getSortedCompartments()) {
+ // draw only compartment that don't have parents (aren't included in any
+ // compartment/complexes)
+ if (compartment.getCompartment() == null) {
+ drawCompartment(compartment);
+ }
+ }
+
+ // draw all layers
+ for (Layer layer : params.getModel().getLayers()) {
+ drawLayer(layer);
+ }
+ closeImageObject();
+ setDrawn(true);
+ }
+
+ /**
+ * Method called after drawing. It should close drawing canvas properly.
+ */
+ protected abstract void closeImageObject();
+
+ /**
+ * This method draw layer on the graphics.
+ *
+ * @param layer
+ * layer to be drawn
+ */
+ private void drawLayer(final Layer layer) {
+ // get a converter nad set text borders to no
+ LayerConverter converter = new LayerConverter(false);
+ converter.drawLayer(layer, graphics);
+ }
+
+ /**
+ * Don't allow to create default public constructors with empty list of
+ * parameters.
+ */
+ protected AbstractImageGenerator() {
+ super();
+ }
+
+ /**
+ * This method draw a {@link Compartment} on a graphics.
+ *
+ * @param compartment
+ * object that we want to draw
+ * @throws DrawingException
+ * thrown when there was a problem with drawing {@link Compartment}
+ */
+ protected void drawCompartment(final Compartment compartment) throws DrawingException {
+ // get a converter for this compartment
+ BioEntityConverterImpl converter = new BioEntityConverterImpl(compartment, colorExtractor);
+ ConverterParams compartmentParams = new ConverterParams().level(level).nested(params.nested);
+
+ if (params.nested) {
+ compartmentParams.scale(Math.max(scale, 1));
+ }
+
+ converter.draw(compartment, graphics, compartmentParams, params.getVisibleLayoutsForElement(compartment));
+
+ // If compartment should be filled, then we could skip drawing the inside
+ // compartments.
+
+ if (zoomLevelMatcher.isTransparent(level, compartment.getTransparencyLevel()) || !params.nested) {
+ List<Element> result = new ArrayList<>();
+ result.addAll(compartment.getElements());
+ Collections.sort(result, Element.SIZE_COMPARATOR);
+
+ // draw all children of this compartment
+ for (Element child : result) {
+ // if a child is a standard species
+ if (child instanceof Species) {
+ drawSpecies((Species) child);
+ } else if (child instanceof Compartment) {
+ drawCompartment((Compartment) child);
+ } else {
+ // if a child is not a compartment or a species then we have a
+ // problem
+ throw new DrawingException(eu.getElementTag(child) + "Unknown Element type");
+ }
+
+ }
+ if (!compartment.containsIdenticalSpecies()) {
+ if (!(compartment instanceof PathwayCompartment)) {
+ converter.drawText(compartment, graphics, compartmentParams);
+ }
+ }
+ }
+ }
+
+ /**
+ * This method draw a {@link Species} on a graphics.
+ *
+ * @param species
+ * object to be drawn
+ * @throws DrawingException
+ * thrown when there was a problem with drawing a {@link Species}
+ */
+ protected void drawSpecies(final Species species) throws DrawingException {
+ if (!cross(species.getBorder())) {
+ return;
+ }
+
+ boolean rescale = false;
+ if (species instanceof Complex) {
+ Complex complex = (Complex) species;
+ if (complex.getElements().size() == 0) {
+ rescale = true;
+ } else {
+ rescale = true;
+ for (Element child : complex.getElements()) {
+ if ((zoomLevelMatcher.isVisible(level, child.getVisibilityLevel())) || !params.nested) {
+ rescale = false;
+ }
+ }
+ }
+ }
+
+ // at the beginning try to find an appropriate converter
+ BioEntityConverterImpl converter = new BioEntityConverterImpl(species, sbgnFormat, colorExtractor);
+ double customScale = 1;
+ if (rescale) {
+ customScale = scale;
+ }
+ converter.draw(species, graphics,
+ new ConverterParams().scale(customScale).level(level).sbgnFormat(sbgnFormat).nested(params.nested),
+ params.getVisibleLayoutsForElement(species));
+
+ // if the species is a complex then we may want to draw children
+ // objects
+ if (species instanceof Complex) {
+ Complex complex = (Complex) species;
+ // before drawing children check if the view is not set to brief
+ // mode
+ if (!complex.getState().equalsIgnoreCase("brief")) {
+ // depending on current zoom level, children are drawn or not
+ if (zoomLevelMatcher.isTransparent(level, complex.getTransparencyLevel()) || !params.nested) {
+ for (Species child : complex.getElements()) {
+ drawSpecies(child);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * This method draw a reaction on a graphics.
+ *
+ * @param reaction
+ * object to be drawn
+ * @throws DrawingException
+ * thrown when there was a problem with drawing a {@link Reaction}
+ */
+ protected void drawReaction(final Reaction reaction) throws DrawingException {
+ if (!cross(reaction.getLines())) {
+ return;
+ }
+ BioEntityConverterImpl converter = new BioEntityConverterImpl(reaction, sbgnFormat, colorExtractor);
+ converter.draw(reaction, graphics, new ConverterParams().sbgnFormat(sbgnFormat).nested(params.nested).level(level),
+ params.getVisibleLayoutsForElement(reaction));
+ }
+
+ /**
+ * Checks if one of the lines in parameter cross the frame.
+ *
+ * @param lines
+ * list of lines to check
+ * @return true if the cross point exist, false otherwise
+ */
+ private boolean cross(final List<Line2D> lines) {
+ for (Line2D line2d : lines) {
+ if (border.intersectsLine(line2d)) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Checks if the rectangle in the parameters cross the fram in which we are
+ * currently draw image.
+ *
+ * @param rect
+ * rectangle to check
+ * @return true if rectangle check the frame, false otherwise
+ */
+ protected boolean cross(final Rectangle2D rect) {
+ return border.intersects(rect);
+ }
+
+ /**
+ * @return the graphics
+ */
+ protected Graphics2D getGraphics() {
+ return graphics;
+ }
+
+ /**
+ * @param graphics
+ * the graphics to set
+ */
+ protected void setGraphics(Graphics2D graphics) {
+ this.graphics = graphics;
+ }
+
+ /**
+ * Saves generated image into file.
+ *
+ * @param fileName
+ * file where the images should be saved
+ * @throws IOException
+ * thrown when there is problem with output file
+ * @throws DrawingException
+ * thrown when there was a problem with drawing map
+ */
+ public final void saveToFile(String fileName) throws IOException, DrawingException {
+ if (!isDrawn()) {
+ draw();
+ }
+ saveToFileImplementation(fileName);
+ };
+
+ /**
+ * Saves generated image from {@link #getGraphics()} into file.
+ *
+ * @param fileName
+ * file where the images should be saved
+ * @throws IOException
+ * thrown when there is problem with output file
+ * @throws DrawingException
+ * thrown when there was a problem with drawing map
+ */
+ protected abstract void saveToFileImplementation(String fileName) throws IOException;
+
+ /**
+ * Saves generated image into {@link OutputStream}.
+ *
+ * @param os
+ * stream where the images should be saved
+ * @throws IOException
+ * thrown when there is problem with output stream
+ * @throws DrawingException
+ * thrown when there was a problem with drawing map
+ */
+ public final void saveToOutputStream(OutputStream os) throws IOException, DrawingException {
+ if (!isDrawn()) {
+ draw();
+ }
+ saveToOutputStreamImplementation(os);
+ }
+
+ /**
+ * Saves generated image from {@link #getGraphics()} into {@link OutputStream} .
+ *
+ * @param os
+ * stream where the images should be saved
+ * @throws IOException
+ * thrown when there is problem with output stream
+ * @throws DrawingException
+ * thrown when there was a problem with drawing map
+ */
+ protected abstract void saveToOutputStreamImplementation(OutputStream os) throws IOException;
+
+ /**
+ * Saves part of the generated image file.
+ *
+ * @param fileName
+ * file where the images should be saved
+ * @param x
+ * x left margin of the image part
+ * @param y
+ * y top margin of the image part
+ * @param width
+ * width of the image part
+ * @param height
+ * hieght of the image part
+ * @throws IOException
+ * thrown when there is problem with output file
+ * @throws DrawingException
+ * thrown when there was a problem with drawing map
+ */
+ public final void savePartToFile(final int x, final int y, final int width, final int height, final String fileName)
+ throws IOException, DrawingException {
+ if (!isDrawn()) {
+ draw();
+ }
+ savePartToFileImplementation(x, y, width, height, fileName);
+ }
+
+ /**
+ * Saves part of the generated image from {@link #getGraphics()} into file.
+ *
+ * @param fileName
+ * file where the images should be saved
+ * @param x
+ * x left margin of the image part
+ * @param y
+ * y top margin of the image part
+ * @param width
+ * width of the image part
+ * @param height
+ * hieght of the image part
+ * @throws IOException
+ * thrown when there is problem with output file
+ */
+ protected abstract void savePartToFileImplementation(final int x, final int y, final int width, final int height,
+ final String fileName) throws IOException;
+
+ /**
+ * Saves part of the generated image into {@link OutputStream}.
+ *
+ * @param os
+ * stream where the images should be saved
+ * @param x
+ * x left margin of the image part
+ * @param y
+ * y top margin of the image part
+ * @param width
+ * width of the image part
+ * @param height
+ * hieght of the image part
+ * @throws IOException
+ * thrown when there is problem with output file
+ * @throws DrawingException
+ * thrown when there was a problem with drawing map
+ */
+ public final void savePartToOutputStream(final int x, final int y, final int width, final int height,
+ final OutputStream os) throws IOException, DrawingException {
+ if (!isDrawn()) {
+ draw();
+ }
+ savePartToOutputStreamImplementation(x, y, width, height, os);
+ }
+
+ /**
+ * Saves part of the generated image from {@link #getGraphics()} into
+ * {@link OutputStream}.
+ *
+ * @param os
+ * stream where the images should be saved
+ * @param x
+ * x left margin of the image part
+ * @param y
+ * y top margin of the image part
+ * @param width
+ * width of the image part
+ * @param height
+ * hieght of the image part
+ * @throws IOException
+ * thrown when there is problem with output file
+ * @throws DrawingException
+ * thrown when there was a problem with drawing map
+ */
+ protected abstract void savePartToOutputStreamImplementation(final int x, final int y, final int width,
+ final int height, final OutputStream os) throws IOException;
+
+ /**
+ * Returns name of the format to which this graphic converter will transform.
+ *
+ * @return name of the format to which this graphic converter will transform
+ */
+ public abstract String getFormatName();
+
+ /**
+ * Returns {@link MimeType} that should be used for files generated by this
+ * image generator.
+ *
+ * @return {@link MimeType} that should be used for files generated by this
+ * image generator
+ */
+ public abstract MimeType getMimeType();
+
+ /**
+ * Returns default file extension used by this image generator.
+ *
+ * @return default file extension used by this image generator
+ */
+ public abstract String getFileExtension();
+
+ /**
+ * @return the sbgnFormat
+ */
+ protected boolean isSbgnFormat() {
+ return sbgnFormat;
+ }
+
+ /**
+ * @param sbgnFormat
+ * the sbgnFormat to set
+ */
+ protected void sbgnFormat(boolean sbgnFormat) {
+ this.sbgnFormat = sbgnFormat;
+ }
+
+ /**
+ * @return the drawn
+ * @see #drawn
+ */
+ private boolean isDrawn() {
+ return drawn;
+ }
+
+ /**
+ * @param drawn
+ * the drawn to set
+ * @see #drawn
+ */
+ private void setDrawn(boolean drawn) {
+ this.drawn = drawn;
+ }
+
+ /**
+ * @return the params
+ * @see #params
+ */
+ protected Params getParams() {
+ return params;
+ }
+
+ /**
+ * @param params
+ * the params to set
+ * @see #params
+ */
+ protected void setParams(Params params) {
+ this.params = params;
+ }
}
\ No newline at end of file
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java
index b8785d7c898ef78eeed77968b982c6bc5ad481c6..f9a9f36ed0415a61ec9683dd56aba9c683488147 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java
@@ -2,8 +2,12 @@ package lcsb.mapviewer.converter.graphics;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
import java.awt.Color;
+import java.awt.Graphics2D;
import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
import java.io.File;
@@ -11,92 +15,126 @@ import java.io.File;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.species.Complex;
-public class PdfImageGeneratorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSaveToFile() throws Exception {
- try {
- String filename = "tmp.pdf";
-
- File f = new File(filename);
- if (f.exists()) {
- f.delete();
- }
-
- assertFalse(f.exists());
-
- Model model = createCompartmentModel();
- Layer layer = model.getLayers().iterator().next();
-
- layer.addLayerText(new LayerText(new Rectangle2D.Double(10, 10, 500, 500), "X asd"));
- layer.addLayerText(new LayerText(new Rectangle2D.Double(20, 20, 200, 200), "Y qwe ret"));
- layer.addLayerText(new LayerText(new Rectangle2D.Double(100, 100, 199, 220), "Z dgf fsd aaewq ret"));
-
- new CreateHierarchyCommand(model, 1, 8).execute();
- model.getCompartments().get(1).setTransparencyLevel("2");
- model.getCompartments().get(0).setTransparencyLevel("2");
- model.getCompartments().get(3).setTransparencyLevel("2");
-
- PdfImageGenerator pig = new PdfImageGenerator(new Params().level(2).scale(4).width(600).height(600).model(model).nested(true));
-
- pig.saveToFile("tmp.pdf");
-
- assertTrue(f.exists());
- f.delete();
- assertFalse(f.exists());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Model createCompartmentModel() {
- Model model = new ModelFullIndexed(null);
- model.setWidth(526);
- model.setHeight(346);
-
- LayerText compAlias = new LayerText();
- compAlias.setX(256.0);
- compAlias.setY(79.0);
- compAlias.setWidth(233.0);
- compAlias.setHeight(188.0);
- compAlias.setNotes("asd as");
- compAlias.setColor(Color.BLACK);
- Layer layer = new Layer();
- layer.addLayerText(compAlias);
- layer.setVisible(true);
- model.addLayer(layer);
-
- layer.addLayerLine(new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(100, 100)));
-
- Complex alias = new Complex("1");
- alias.setName("a");
- alias.setX(300);
- alias.setY(90);
- alias.setWidth(100);
- alias.setHeight(50);
- model.addElement(alias);
-
- return model;
- }
+public class PdfImageGeneratorTest extends GraphicsTestFunctions {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSaveToFile() throws Exception {
+ try {
+ String filename = "tmp.pdf";
+
+ File f = new File(filename);
+ if (f.exists()) {
+ f.delete();
+ }
+
+ assertFalse(f.exists());
+
+ Model model = createCompartmentModel();
+ Layer layer = model.getLayers().iterator().next();
+
+ layer.addLayerText(new LayerText(new Rectangle2D.Double(10, 10, 500, 500), "X asd"));
+ layer.addLayerText(new LayerText(new Rectangle2D.Double(20, 20, 200, 200), "Y qwe ret"));
+ layer.addLayerText(new LayerText(new Rectangle2D.Double(100, 100, 199, 220), "Z dgf fsd aaewq ret"));
+
+ new CreateHierarchyCommand(model, 1, 8).execute();
+ model.getCompartments().get(1).setTransparencyLevel("2");
+ model.getCompartments().get(0).setTransparencyLevel("2");
+ model.getCompartments().get(3).setTransparencyLevel("2");
+
+ PdfImageGenerator pig = createAbstractImageGeneratorMock(model, null);
+
+ pig.saveToFile("tmp.pdf");
+
+ assertTrue(f.exists());
+ f.delete();
+ assertFalse(f.exists());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private PdfImageGenerator createAbstractImageGeneratorMock(Model model, Graphics2D graphics) throws DrawingException {
+ PdfImageGenerator pig = new PdfImageGenerator(
+ new Params().level(2).scale(4).width(600).height(600).model(model).nested(true));
+ if (graphics != null) {
+ pig.setGraphics(graphics);
+ }
+ return Mockito.spy(pig);
+ }
+
+ private Model createCompartmentModel() {
+ Model model = new ModelFullIndexed(null);
+ model.setWidth(526);
+ model.setHeight(346);
+
+ LayerText compAlias = new LayerText();
+ compAlias.setX(256.0);
+ compAlias.setY(79.0);
+ compAlias.setWidth(233.0);
+ compAlias.setHeight(188.0);
+ compAlias.setNotes("asd as");
+ compAlias.setColor(Color.BLACK);
+ Layer layer = new Layer();
+ layer.addLayerText(compAlias);
+ layer.setVisible(true);
+ model.addLayer(layer);
+
+ layer.addLayerLine(new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(100, 100)));
+
+ Complex alias = new Complex("1");
+ alias.setName("a");
+ alias.setX(300);
+ alias.setY(90);
+ alias.setWidth(100);
+ alias.setHeight(50);
+ model.addElement(alias);
+
+ return model;
+ }
+
+ @Test
+ public void testDrawPathwayWithoutNesting() throws Exception {
+ try {
+ Graphics2D graphics = createGraphicsMock();
+
+ Model model = createCompartmentModel();
+
+ PathwayCompartment pathway = new PathwayCompartment("id");
+ pathway.setWidth(100);
+ pathway.setHeight(100);
+ model.addElement(pathway);
+ AbstractImageGenerator gen = createAbstractImageGeneratorMock(model, graphics);
+ gen.getParams().nested(false);
+ gen.drawCompartment(pathway);
+
+ // 3 times for proteins and 4 times for reaction
+ verify(graphics, times(1)).draw(any());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
index 0f9972fd83a2d9f993b9b9b4515a6296126ed638..8f630430f001d5675aaabb8b031cf18d5035623f 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
@@ -117,7 +117,7 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends
return elementWithLayout;
}
- private void applyStyleToElement(Element elementWithLayout, LocalStyle style) {
+ protected void applyStyleToElement(Element elementWithLayout, LocalStyle style) {
if (style.getGroup().getFill() != null) {
Color backgroundColor = getColorByColorDefinition(style.getGroup().getFill());
elementWithLayout.setColor(backgroundColor);
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
index 5501b2aa09c79d1dac5d6183f08ce41a30ffe711..3d860fecee9bbe994a4011e7674ffc9c333979fd 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
@@ -16,6 +16,7 @@ import org.sbml.jsbml.ext.render.RenderLayoutPlugin;
import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionExporter;
import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesExporter;
+import lcsb.mapviewer.converter.model.sbml.units.SbmlUnitExporter;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.species.Species;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
index 7472ee1cbb776bfb8d42484d2f335210ff00e461..84188fea079695c04a0123166fecb8df867158d3 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -31,6 +31,7 @@ import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionParser;
import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesParser;
+import lcsb.mapviewer.converter.model.sbml.units.SbmlUnitsParser;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.MiriamData;
@@ -40,7 +41,9 @@ import lcsb.mapviewer.model.map.modifier.Modulation;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.Modifier;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
public class SbmlParser implements IConverter {
@@ -115,6 +118,9 @@ public class SbmlParser implements IConverter {
if (sbmlModel.getRuleCount() > 0) {
throw new NotImplementedException("Rule not implemented for model");
}
+ if (layoutExists) {
+ addComplexRelationsBasedOnCoordinates(model);
+ }
createLayout(model, layout, params.isSizeAutoAdjust(), reactionParser);
return model;
} catch (XMLStreamException e) {
@@ -122,6 +128,39 @@ public class SbmlParser implements IConverter {
}
}
+ private void addComplexRelationsBasedOnCoordinates(Model model) {
+ for (Element element : model.getElements()) {
+ if (element instanceof Species) {
+ Species species = (Species) element;
+ if (species.getComplex() == null && element.getWidth() != 0 || element.getHeight() != 0) {
+ Complex complex = findComplexForElement(species, model);
+ if (complex != null) {
+ complex.addSpecies(species);
+ }
+ }
+ }
+ }
+ }
+
+ private Complex findComplexForElement(Species species, Model model) {
+ Complex result = null;
+ for (Element element : model.getElements()) {
+ if (element instanceof Complex && element != species) {
+ Complex complex = (Complex) element;
+ if (complex.getWidth() != 0 || complex.getHeight() != 0) {
+ if (complex.contains(species)) {
+ if (result == null) {
+ result = complex;
+ } else if (result.getSize() > complex.getSize()) {
+ result = complex;
+ }
+ }
+ }
+ }
+ }
+ return result;
+ }
+
private void createLayout(Model model, Layout layout, boolean resize, SbmlReactionParser parser)
throws InvalidInputDataExecption {
if (model.getWidth() == null) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
index 28b6c80aff8c4317fa08c8b37f6f6ee7981323d7..81430191709ceffeb02c6a7817e30ef823a4d25b 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
@@ -188,7 +188,7 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
reactantGlyph.setRole(SpeciesReferenceRole.SUBSTRATE);
for (NodeOperator operator : reaction.getOperators()) {
if (operator.isReactantOperator()) {
- addOperatorLineToGlyph(reactionGlyph, operator, true);
+ addOperatorLineToGlyph(reactionGlyph, operator, false);
if (reactantEndPoint == null) {
reactantEndPoint = operator.getLine().getEndPoint();
}
@@ -274,7 +274,7 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
private SpeciesReferenceGlyph createNodeGlyph(ReactionGlyph reactionGlyph, ReactionNode node) {
SpeciesReferenceGlyph reactantGlyph = reactionGlyph.createSpeciesReferenceGlyph("node_" + getNextId());
reactantGlyph.setSpeciesGlyph(speciesExporter.getSbmlGlyphByElementId(node.getElement().getElementId()).getId());
- reactantGlyph.setCurve(createCurve(node, node instanceof Reactant));
+ reactantGlyph.setCurve(createCurve(node, false));
reactantGlyph.setSpeciesReference(speciesReferenceByReactionNode.get(node));
return reactantGlyph;
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
index e02e9b12d4db8b66bb0682cc4a806c63d91666e2..78f4e55e4d9a4b500861c0c5af1a3d787e3b01c9 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
@@ -47,6 +47,7 @@ import lcsb.mapviewer.model.map.modifier.Modulation;
import lcsb.mapviewer.model.map.modifier.Trigger;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.AndOperator;
+import lcsb.mapviewer.model.map.reaction.AssociationOperator;
import lcsb.mapviewer.model.map.reaction.Modifier;
import lcsb.mapviewer.model.map.reaction.NodeOperator;
import lcsb.mapviewer.model.map.reaction.Product;
@@ -54,6 +55,7 @@ import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
import lcsb.mapviewer.model.map.reaction.SplitOperator;
+import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
@@ -145,14 +147,11 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
+ " in reaction " + reactionWithLayout.getElementId());
}
if (minervaNode instanceof Reactant) {
- line = line.reverse();
- line.addPoint(line.getEndPoint());
if (reactionWithLayout.isReversible()) {
line.getBeginAtd().setArrowType(ArrowType.FULL);
}
}
if (minervaNode instanceof Product) {
- line.addPoint(0, line.getBeginPoint());
ArrowTypeData atd = new ArrowTypeData();
atd.setArrowType(ArrowType.FULL);
line.setEndAtd(atd);
@@ -187,15 +186,7 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
}
}
if (reactionWithLayout.getReactants().size() > 1 && reactionWithLayout.getProducts().size() > 0) {
- PolylineData line = new PolylineData();
- Point2D p1 = reactionWithLayout.getReactants().get(0).getLine().getEndPoint();
- Point2D p2 = reactionWithLayout.getProducts().get(0).getLine().getBeginPoint();
- Point2D center = new Point2D.Double((p1.getX() + p2.getX()) / 2, (p1.getY() + p2.getY()) / 2);
- line.addPoint(p1);
- line.addPoint(center);
- NodeOperator operator = new AndOperator();
- operator.addInputs(reactionWithLayout.getReactants());
- operator.setLine(line);
+ NodeOperator operator = createInputOperator(reactionWithLayout);
reactionWithLayout.addNode(operator);
}
if (reactionWithLayout.getReactants().size() > 0 && reactionWithLayout.getProducts().size() > 1) {
@@ -234,6 +225,24 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
}
}
+ private NodeOperator createInputOperator(Reaction reactionWithLayout) {
+ PolylineData line = new PolylineData();
+ Point2D p1 = reactionWithLayout.getReactants().get(0).getLine().getEndPoint();
+ Point2D p2 = reactionWithLayout.getProducts().get(0).getLine().getBeginPoint();
+ Point2D center = new Point2D.Double((p1.getX() + p2.getX()) / 2, (p1.getY() + p2.getY()) / 2);
+ line.addPoint(p1);
+ line.addPoint(center);
+ NodeOperator operator ;
+ if (reactionWithLayout instanceof HeterodimerAssociationReaction) {
+ operator = new AssociationOperator();
+ } else {
+ operator = new AndOperator();
+ }
+ operator.addInputs(reactionWithLayout.getReactants());
+ operator.setLine(line);
+ return operator;
+ }
+
private Class<? extends ReactionNode> getReactionNodeClass(SpeciesReferenceGlyph speciesRefernceGlyph) {
Class<? extends ReactionNode> nodeClass = null;
if (speciesRefernceGlyph.getRole() != null) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
index f7a11fe45eb09418efcc658c7ad71534a834fac3..dba417b2738f687400dc32e25ea076b234e8eb52 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
@@ -5,6 +5,7 @@ import java.util.List;
import org.apache.log4j.Logger;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.ext.render.LocalStyle;
import lcsb.mapviewer.converter.model.sbml.SbmlCompartmentExporter;
import lcsb.mapviewer.converter.model.sbml.SbmlElementExporter;
@@ -28,6 +29,9 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
if (element.getCompartment() != null) {
result.setCompartment(compartmentExporter.getSbmlElement(element.getCompartment()));
}
+ if (element.getInitialAmount() != null) {
+ result.setInitialAmount(element.getInitialAmount());
+ }
return result;
}
@@ -45,10 +49,20 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
@Override
protected String getSbmlIdKey(Species element) {
String compartmentName = null;
+ String complexName = null;
if (element.getCompartment() != null) {
compartmentName = element.getCompartment().getName();
}
- return element.getClass().getSimpleName() + "\n" + element.getName() + "\n" + compartmentName;
+ if (element.getComplex() != null) {
+ complexName = element.getComplex().getName();
+ }
+ return element.getClass().getSimpleName() + "\n" + element.getName() + "\n" + compartmentName+ "\n" + complexName;
+ }
+
+ protected LocalStyle createStyle(Species element) {
+ LocalStyle style = super.createStyle(element);
+ style.getGroup().setStrokeWidth(element.getLineWidth());
+ return style;
}
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
index 07a3d675f7d6710ed737c90cb33690f0ab5c554f..c17c23765e6b96ef4e29f3a242395b22d58f82b5 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
@@ -11,6 +11,7 @@ import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
import org.sbml.jsbml.ext.layout.CompartmentGlyph;
import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.SpeciesGlyph;
+import org.sbml.jsbml.ext.render.LocalStyle;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidStateException;
@@ -33,6 +34,9 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
Class<? extends Species> clazz = SBOTermSpeciesType.getTypeSBOTerm(sboTerm);
try {
Species result = clazz.getConstructor(String.class).newInstance(species.getId());
+ if (!Double.isNaN(species.getInitialAmount())) {
+ result.setInitialAmount(species.getInitialAmount());
+ }
assignBioEntityData(species, result);
if (layout == null) {
assignCompartment(result, species.getCompartment());
@@ -98,4 +102,13 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
return result;
}
+ @Override
+ protected void applyStyleToElement(Element elementWithLayout, LocalStyle style) {
+ super.applyStyleToElement(elementWithLayout, style);
+ Species specisWithLayout = (Species) elementWithLayout;
+ if (style.getGroup().isSetStrokeWidth()) {
+ specisWithLayout.setLineWidth(style.getGroup().getStrokeWidth());
+ }
+ }
+
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlUnitExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/SbmlUnitExporter.java
similarity index 54%
rename from converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlUnitExporter.java
rename to converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/SbmlUnitExporter.java
index 27e2fa310ddea6c3feadf7b33112663190ad741c..5d5777805927657337a01c0bd3f78c5aff424063 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlUnitExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/SbmlUnitExporter.java
@@ -1,13 +1,16 @@
-package lcsb.mapviewer.converter.model.sbml;
+package lcsb.mapviewer.converter.model.sbml.units;
import org.apache.log4j.Logger;
+import org.sbml.jsbml.Unit;
import org.sbml.jsbml.UnitDefinition;
import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitTypeFactor;
import lcsb.mapviewer.model.map.model.Model;
public class SbmlUnitExporter {
- Logger logger = Logger.getLogger(SbmlUnitExporter.class);
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SbmlUnitExporter.class);
private Model minervaModel;
public SbmlUnitExporter(lcsb.mapviewer.model.map.model.Model minervaModel) {
@@ -24,6 +27,14 @@ public class SbmlUnitExporter {
UnitDefinition result = new UnitDefinition();
result.setId(unit.getUnitId());
result.setName(unit.getName());
+ for (SbmlUnitTypeFactor factor : unit.getUnitTypeFactors()) {
+ Unit sbmlUnit = new Unit();
+ sbmlUnit.setKind(UnitMapping.unitTypeToKind(factor.getUnitType()));
+ sbmlUnit.setExponent((double) factor.getExponent());
+ sbmlUnit.setMultiplier(factor.getMultiplier());
+ sbmlUnit.setScale(factor.getScale());
+ result.addUnit(sbmlUnit);
+ }
return result;
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlUnitsParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/SbmlUnitsParser.java
similarity index 66%
rename from converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlUnitsParser.java
rename to converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/SbmlUnitsParser.java
index 60b65e25ea57ad6ec5613fd69143358caaec7f82..bd5ad0057638392210912b66caf947d1a49dbd27 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlUnitsParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/SbmlUnitsParser.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.model.sbml;
+package lcsb.mapviewer.converter.model.sbml.units;
import java.util.ArrayList;
import java.util.Collection;
@@ -7,8 +7,11 @@ import java.util.List;
import org.apache.log4j.Logger;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.Model;
+import org.sbml.jsbml.Unit;
+import lcsb.mapviewer.converter.model.sbml.SbmlBioEntityParser;
import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitTypeFactor;
public class SbmlUnitsParser extends SbmlBioEntityParser {
Logger logger = Logger.getLogger(SbmlUnitsParser.class);
@@ -20,6 +23,12 @@ public class SbmlUnitsParser extends SbmlBioEntityParser {
protected SbmlUnit parse(org.sbml.jsbml.UnitDefinition unitDefinition, Model sbmlModel) {
SbmlUnit result = new SbmlUnit(unitDefinition.getId());
result.setName(unitDefinition.getName());
+ for (int i = 0; i < unitDefinition.getUnitCount(); i++) {
+ Unit sbmlUnit = unitDefinition.getUnit(i);
+ SbmlUnitTypeFactor factor = new SbmlUnitTypeFactor(UnitMapping.kindToUnitType(sbmlUnit.getKind()),
+ (int) sbmlUnit.getExponent(), sbmlUnit.getScale(), sbmlUnit.getMultiplier());
+ result.addUnitTypeFactor(factor);
+ }
return result;
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/UnitMapping.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/UnitMapping.java
new file mode 100644
index 0000000000000000000000000000000000000000..4a75ac6ea5a4472d9394c4bd797064b602f2aae6
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/UnitMapping.java
@@ -0,0 +1,97 @@
+package lcsb.mapviewer.converter.model.sbml.units;
+
+import org.sbml.jsbml.Unit.Kind;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
+
+public enum UnitMapping {
+ AMPERE(SbmlUnitType.AMPERE, Kind.AMPERE),
+
+ BECQUEREL(SbmlUnitType.BECQUEREL, Kind.BECQUEREL),
+
+ CANDELA(SbmlUnitType.CANDELA, Kind.CANDELA),
+
+ COULUMB(SbmlUnitType.COULUMB, Kind.COULOMB),
+
+ DIMENSIONLESS(SbmlUnitType.DIMENSIONLESS, Kind.DIMENSIONLESS),
+
+ FARAD(SbmlUnitType.FARAD, Kind.FARAD),
+
+ GRAM(SbmlUnitType.GRAM, Kind.GRAM),
+
+ GRAY(SbmlUnitType.GRAY, Kind.GRAY),
+
+ HENRY(SbmlUnitType.HENRY, Kind.HENRY),
+
+ HERTZ(SbmlUnitType.HERTZ, Kind.HERTZ),
+
+ ITEM(SbmlUnitType.ITEM, Kind.ITEM),
+
+ JOULE(SbmlUnitType.JOULE, Kind.JOULE),
+
+ KATAL(SbmlUnitType.KATAL, Kind.KATAL),
+
+ KELVIN(SbmlUnitType.KELVIN, Kind.KELVIN),
+
+ KILOGRAM(SbmlUnitType.KILOGRAM, Kind.KILOGRAM),
+
+ LITRE(SbmlUnitType.LITRE, Kind.LITRE),
+
+ LUMEN(SbmlUnitType.LUMEN, Kind.LUMEN),
+
+ LUX(SbmlUnitType.LUX, Kind.LUX),
+
+ METRE(SbmlUnitType.METRE, Kind.METRE),
+
+ MOLE(SbmlUnitType.MOLE, Kind.MOLE),
+
+ NEWTON(SbmlUnitType.NEWTON, Kind.NEWTON),
+
+ OHM(SbmlUnitType.OHM, Kind.OHM),
+
+ PASCAL(SbmlUnitType.PASCAL, Kind.PASCAL),
+
+ RADIAN(SbmlUnitType.RADIAN, Kind.RADIAN),
+
+ SECOND(SbmlUnitType.SECOND, Kind.SECOND),
+
+ SIEMENS(SbmlUnitType.SIEMENS, Kind.SIEMENS),
+
+ SIEVERT(SbmlUnitType.SIEVERT, Kind.SIEVERT),
+
+ STERADIAN(SbmlUnitType.STERADIAN, Kind.STERADIAN),
+
+ TESLA(SbmlUnitType.TESLA, Kind.TESLA),
+
+ VOLT(SbmlUnitType.VOLT, Kind.VOLT),
+
+ WATT(SbmlUnitType.WATT, Kind.WATT),
+
+ WEBER(SbmlUnitType.WEBER, Kind.WEBER);
+
+ private SbmlUnitType unitType;
+ private Kind sbmlUnitType;
+
+ UnitMapping(SbmlUnitType unitType, Kind sbmlUnitType) {
+ this.unitType = unitType;
+ this.sbmlUnitType = sbmlUnitType;
+ }
+
+ public static Kind unitTypeToKind(SbmlUnitType unitType) {
+ for (UnitMapping mapping : UnitMapping.values()) {
+ if (mapping.unitType == unitType) {
+ return mapping.sbmlUnitType;
+ }
+ }
+ throw new InvalidArgumentException("Unknown sbml unit type: " + unitType);
+ }
+ public static SbmlUnitType kindToUnitType(Kind kind) {
+ for (UnitMapping mapping : UnitMapping.values()) {
+ if (mapping.sbmlUnitType == kind) {
+ return mapping.unitType;
+ }
+ }
+ throw new InvalidArgumentException("Unknown sbml unit type: " + kind);
+ }
+}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
index faddef001b703cea2550f3bf93c6faa1d7bb596c..a4ee68a74ff8a97f533dd669f07fc5d639a17bae 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
@@ -14,6 +14,7 @@ import lcsb.mapviewer.converter.model.sbml.species.AllSbmlSpeciesTests;
GenericSbmlToXmlParserTest.class,
SbmlBioEntityExporterTest.class,
SbmlExporterTest.class,
+ SbmlExporterFromCellDesignerTest.class,
SbmlPareserForInvalidReactionTest.class,
SbmlParserTest.class,
})
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterFromCellDesignerTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterFromCellDesignerTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..db0bfcba1451743661fa16f0834238e894d3ab98
--- /dev/null
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterFromCellDesignerTest.java
@@ -0,0 +1,80 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import static org.junit.Assert.assertEquals;
+
+import java.awt.Desktop;
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.nio.file.Files;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
+import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
+import lcsb.mapviewer.converter.graphics.PngImageGenerator;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class SbmlExporterFromCellDesignerTest {
+ Logger logger = Logger.getLogger(SbmlExporterFromCellDesignerTest.class);
+ SbmlParser parser = new SbmlParser();
+ SbmlExporter exporter = new SbmlExporter();
+
+ CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
+
+ ModelComparator comparator = new ModelComparator();
+
+ @Test
+ public void testExportHeterodimerAssociation() throws Exception {
+ try {
+ Model originalModel = cellDesignerXmlParser
+ .createModel(new ConverterParams().filename("testFiles/cell_designer_problems/heterodimer_association.xml"));
+ Model model = getModelAfterSerializing(originalModel);
+ Reaction reaction1 = originalModel.getReactions().iterator().next();
+ Reaction reaction2 = model.getReactions().iterator().next();
+ //change reaction id - due to some issues it cannot be persisted properly in sbml format
+ reaction2.setIdReaction(reaction1.getIdReaction());
+
+ model.setName(originalModel.getName());
+
+ String cellDesignerXml = cellDesignerXmlParser.toXml(model);
+ ByteArrayInputStream stream = new ByteArrayInputStream(cellDesignerXml.getBytes("UTF-8"));
+
+ assertEquals(0, comparator.compare(model, originalModel));
+ Model cdModel = cellDesignerXmlParser.createModel(new ConverterParams().inputStream(stream));
+
+ cdModel.setName(originalModel.getName());
+
+ assertEquals(0, comparator.compare(model, cdModel));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model getModelAfterSerializing(Model originalModel) throws Exception {
+ String xml = exporter.toXml(originalModel);
+// logger.debug(xml);
+ ByteArrayInputStream stream = new ByteArrayInputStream(xml.getBytes("UTF-8"));
+ Model result = parser.createModel(new ConverterParams().inputStream(stream));
+ // showImage(originalModel);
+ // showImage(result);
+ return result;
+ }
+
+ protected void showImage(Model model) throws Exception {
+ String dir = Files.createTempDirectory("sbml-temp-images-dir").toFile().getAbsolutePath();
+ AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().height(model.getHeight())
+ .width(model.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model);
+ NormalImageGenerator nig = new PngImageGenerator(params);
+ String pathWithouExtension = dir + "/" + model.getName();
+ String pngFilePath = pathWithouExtension.concat(".png");
+ nig.saveToFile(pngFilePath);
+ Desktop.getDesktop().open(new File(pngFilePath));
+
+ }
+}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java
index 3951251a80a176ac2e88f7b4dbf2abae7fe3f82b..99fd30b620d0a1e04ad903aaab9975a434516b1d 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java
@@ -26,6 +26,7 @@ import lcsb.mapviewer.model.map.species.Phenotype;
import lcsb.mapviewer.model.map.species.ReceptorProtein;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.Unknown;
public class SbmlSpeciesParserTest {
@@ -144,4 +145,11 @@ public class SbmlSpeciesParserTest {
assertTrue(element instanceof Unknown);
assertEquals(ElementColorEnum.UNKNOWN.getColor(), element.getColor());
}
+
+ @Test
+ public void testParseInitialAmount() throws Exception {
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/small/initial_amount.xml"));
+ Species element = model.getElementByElementId("s1");
+ assertEquals((Double)1.0, element.getInitialAmount());
+ }
}
diff --git a/converter-sbml/src/test/resources/log4j.properties b/converter-sbml/src/test/resources/log4j.properties
index 37b21cdca50e2c85da60b1de7c3cafa82296d30f..ba8ff0be96889d17faa34dd80f98ae2bb5cf3253 100644
--- a/converter-sbml/src/test/resources/log4j.properties
+++ b/converter-sbml/src/test/resources/log4j.properties
@@ -17,6 +17,7 @@ log4j.appender.R.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
log4j.logger.org.springframework=warn
log4j.logger.org.hibernate=warn
+log4j.logger.org.sbml.jsbml=info
log4j.logger.lcsb=debug
log4j.logger.lcsb.mapviewer.common.comparator=info
diff --git a/converter-sbml/testFiles/cell_designer_problems/heterodimer_association.xml b/converter-sbml/testFiles/cell_designer_problems/heterodimer_association.xml
new file mode 100644
index 0000000000000000000000000000000000000000..a27ccb421344eade985488b338ac33d54e34e725
--- /dev/null
+++ b/converter-sbml/testFiles/cell_designer_problems/heterodimer_association.xml
@@ -0,0 +1,277 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfIncludedSpecies>
+<celldesigner:species id="s4" name="s1">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s3</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s5" name="s2">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s3</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+</celldesigner:listOfIncludedSpecies>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases>
+<celldesigner:complexSpeciesAlias id="csa1" species="s3">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="325.0" y="119.0" w="100.0" h="120.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="100.0" height="120.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
+</celldesigner:listOfComplexSpeciesAliases>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="155.0" y="129.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa2" species="s2">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="155.0" y="189.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa3" species="s4" complexSpeciesAlias="csa1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="335.0" y="129.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10.0" y="10.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa4" species="s5" complexSpeciesAlias="csa1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="335.0" y="179.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10.0" y="60.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s1" type="GENERIC"/>
+<celldesigner:protein id="pr2" name="s2" type="GENERIC"/>
+</celldesigner:listOfProteins>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00006" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00007" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00008" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s3" id="s3" name="s3" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>s3</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+<listOfReactions>
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+<celldesigner:baseReactant species="s2" alias="sa2">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s3" alias="csa1">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection arm="0" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints num0="0" num1="0" num2="0" tShapeIndex="0">0.2944444444444443,0.4111111111111114</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00003" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>csa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+</listOfReactions>
+</model>
+</sbml>
diff --git a/converter-sbml/testFiles/small/initial_amount.xml b/converter-sbml/testFiles/small/initial_amount.xml
new file mode 100644
index 0000000000000000000000000000000000000000..f4c3fe97b28e07d4b5fe14d0c1e861724cff4646
--- /dev/null
+++ b/converter-sbml/testFiles/small/initial_amount.xml
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+ <model id="TestGEN">
+ <annotation/>
+ <listOfCompartments>
+ <compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+ <rdf:Description rdf:about="#">
+ <bqbiol:isVersionOf>
+ <rdf:Bag>
+ <rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
+ </rdf:Bag>
+ </bqbiol:isVersionOf>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </compartment>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species boundaryCondition="false" compartment="cell" initialConcentration="1" id="s1" name="nm1" sboTerm="SBO:0000247" initialAmount="1">
+ <annotation/>
+ </species>
+ </listOfSpecies>
+ </model>
+</sbml>
\ No newline at end of file
diff --git a/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js b/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
index 1d27c67effa437ae52060163f427b0b0ab0e5ed6..daf5a05285bbdcbeeaed9f4aed0981711ffcecc8 100644
--- a/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
@@ -6,6 +6,8 @@ var Promise = require("bluebird");
var AbstractDbPanel = require('./AbstractDbPanel');
var Alias = require('../../map/data/Alias');
+var ConfigurationType = require('../../ConfigurationType');
+var GuiConnector = require('../../GuiConnector');
var IdentifiedElement = require('../../map/data/IdentifiedElement');
var InvalidArgumentError = require('../../InvalidArgumentError');
var PanelControlElementType = require('../PanelControlElementType');
@@ -19,16 +21,17 @@ var Functions = require('../../Functions');
/**
*
* @param params
+ * @param {Configuration} params.configuration
* @constructor
* @extends AbstractDbPanel
*/
function GenericSearchPanel(params) {
var self = this;
- params.panelName = "search";
- params.helpTip = "<p>search tab allows to search for particular elements or interactions in the map</p>"
+ params["panelName"] = "search";
+ params["helpTip"] = "<p>search tab allows to search for particular elements or interactions in the map</p>"
+ "<p>perfect match tick box active: only terms with an exact match to the query will be returned</p>"
+ "<p>separate multiple search by semicolon</p>";
- params.placeholder = "keyword";
+ params["placeholder"] = "keyword";
AbstractDbPanel.call(self, params);
@@ -190,7 +193,16 @@ GenericSearchPanel.prototype.searchByQuery = function () {
var self = this;
var query = this.getControlElement(PanelControlElementType.SEARCH_INPUT).value;
var perfect = this.getControlElement(PanelControlElementType.SEARCH_PERFECT_MATCH_CHECKBOX).checked;
- return self.getOverlayDb().searchByQuery(query, perfect, true);
+ return self.getOverlayDb().searchByQuery(query, perfect, true).then(function (result) {
+ var max = 0;
+ for (var i = 0; i < result.length; i++) {
+ max = Math.max(max, result[i].length);
+ }
+ if (max >= parseInt(self.getConfiguration().getOption(ConfigurationType.SEARCH_RESULT_NUMBER).getValue())) {
+ GuiConnector.warn("Max number of results is exceeded - some results are omitted; " +
+ "please narrow you criteria to see all results or use 'perfect match'");
+ }
+ });
};
/**
diff --git a/frontend-js/src/test/js/gui/leftPanel/GenericSearchPanel-test.js b/frontend-js/src/test/js/gui/leftPanel/GenericSearchPanel-test.js
index 34200db33ff6af90d16155a5885a8c3db1855862..bf5a311991c2e1da854ddf82ec5636ddb4b604fb 100644
--- a/frontend-js/src/test/js/gui/leftPanel/GenericSearchPanel-test.js
+++ b/frontend-js/src/test/js/gui/leftPanel/GenericSearchPanel-test.js
@@ -15,7 +15,7 @@ var assert = chai.assert;
var logger = require('../../logger');
describe('GenericSearchPanel', function () {
- /**t
+ /**
*
* @param {CustomMap} [map]
* @returns {GenericSearchPanel}
@@ -29,7 +29,8 @@ describe('GenericSearchPanel', function () {
return new GenericSearchPanel({
element: testDiv,
- customMap: map
+ customMap: map,
+ configuration: helper.getConfiguration()
});
};
@@ -39,7 +40,8 @@ describe('GenericSearchPanel', function () {
new GenericSearchPanel({
element: testDiv,
- customMap: map
+ customMap: map,
+ configuration: helper.getConfiguration()
});
assert.equal(logger.getWarnings().length, 0);
});
@@ -52,12 +54,9 @@ describe('GenericSearchPanel', function () {
var map = helper.createCustomMap();
map.getModel().setId(15781);
- var searchDbOverlay = helper.createSearchDbOverlay(map);
- new GenericSearchPanel({
- element: testDiv,
- customMap: map
- });
+ createPanel(map);
+ var searchDbOverlay = map.getOverlayByName("search");
var searchParams = {
modelId: map.getModel().getId(),
@@ -76,12 +75,8 @@ describe('GenericSearchPanel', function () {
it('on searchResults changed 2', function () {
var map = helper.createCustomMap();
map.getModel().setId(15781);
- var searchDbOverlay = helper.createSearchDbOverlay(map);
-
- new GenericSearchPanel({
- element: testDiv,
- customMap: map
- });
+ createPanel(map);
+ var searchDbOverlay = map.getOverlayByName("search");
return searchDbOverlay.searchByQuery("s1", false).then(function () {
assert.equal(logger.getWarnings().length, 0);
@@ -92,12 +87,7 @@ describe('GenericSearchPanel', function () {
it('search by query with no results', function () {
var map = helper.createCustomMap();
map.getModel().setId(15781);
- helper.createSearchDbOverlay(map);
-
- var panel = new GenericSearchPanel({
- element: testDiv,
- customMap: map
- });
+ var panel = createPanel(map);
panel.getControlElement(PanelControlElementType.SEARCH_INPUT).value = "s1";
@@ -113,12 +103,7 @@ describe('GenericSearchPanel', function () {
it('visible', function () {
helper.getConfiguration().getOption(ConfigurationType.SHOW_REACTION_TYPE).setValue("true");
var map = helper.createCustomMap();
- helper.createSearchDbOverlay(map);
-
- var panel = new GenericSearchPanel({
- element: testDiv,
- customMap: map
- });
+ var panel = createPanel(map);
var reaction = helper.createReaction(map);
var reactionType = "XX TYPE";
reaction.setType(reactionType);
@@ -131,12 +116,7 @@ describe('GenericSearchPanel', function () {
it('invisible', function () {
helper.getConfiguration().getOption(ConfigurationType.SHOW_REACTION_TYPE).setValue("true");
var map = helper.createCustomMap();
- helper.createSearchDbOverlay(map);
-
- var panel = new GenericSearchPanel({
- element: testDiv,
- customMap: map
- });
+ var panel = createPanel(map);
var reaction = helper.createReaction(map);
var reactionType = "XX TYPE";
reaction.setType(reactionType);
@@ -154,7 +134,6 @@ describe('GenericSearchPanel', function () {
describe('createAliasElement', function () {
it('default', function () {
var map = helper.createCustomMap();
- helper.createSearchDbOverlay(map);
var aliasObj = {
symbol: "S1_SYMBOL",
@@ -178,10 +157,7 @@ describe('GenericSearchPanel', function () {
var alias = new Alias(aliasObj);
- var panel = new GenericSearchPanel({
- element: testDiv,
- customMap: map
- });
+ var panel = createPanel(map);
return panel.createAliasElement(alias).then(function (aliasDiv) {
assert.ok(aliasDiv.innerHTML);
@@ -197,12 +173,7 @@ describe('GenericSearchPanel', function () {
};
var map = helper.createCustomMap();
- helper.createSearchDbOverlay(map);
-
- var panel = new GenericSearchPanel({
- element: testDiv,
- customMap: map
- });
+ var panel = createPanel(map);
var alias = helper.createAlias(map);
alias.setFullName("xxx");
@@ -216,12 +187,7 @@ describe('GenericSearchPanel', function () {
it('invisible', function () {
var map = helper.createCustomMap();
- helper.createSearchDbOverlay(map);
-
- var panel = new GenericSearchPanel({
- element: testDiv,
- customMap: map
- });
+ var panel = createPanel(map);
var alias = helper.createAlias(map);
alias.setFullName("");
@@ -236,12 +202,7 @@ describe('GenericSearchPanel', function () {
describe('clear', function () {
it('input text', function () {
var map = helper.createCustomMap();
- helper.createSearchDbOverlay(map);
-
- new GenericSearchPanel({
- element: testDiv,
- customMap: map
- });
+ var panel = createPanel(map);
$(".typeahead", testDiv)[0].value = "some input";
return map.clearDbOverlays().then(function () {
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
index e9c36488291281e137c013eb169494cc7b015b52..6978f949492188606de1ab858091de4d772ab996 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
@@ -25,11 +25,14 @@ import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.AndOperator;
+import lcsb.mapviewer.model.map.reaction.AssociationOperator;
import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.SplitOperator;
+import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
@@ -240,9 +243,13 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
}
private void modifyReactants(Reaction reaction, Point2D middle) {
- AndOperator operator = null;
+ NodeOperator operator = null;
if (reaction.getReactants().size() > 1) {
- operator = new AndOperator();
+ if (reaction instanceof HeterodimerAssociationReaction) {
+ operator = new AssociationOperator();
+ } else {
+ operator = new AndOperator();
+ }
Point2D productPoint = reaction.getReactants().get(0).getElement().getCenter();
Point2D operatorPoint = getMiddlePoint(middle, productPoint);
operator.setLine(new PolylineData(middle, operatorPoint));
diff --git a/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java b/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java
index e9d0dc743498a316c35cc429a5e19060177282c9..4c5479327a78b9d6ea9398e702599db03c4b5a8e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java
@@ -26,6 +26,7 @@ import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
import org.hibernate.annotations.Type;
+import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.common.geometry.PointTransformation;
@@ -282,7 +283,10 @@ public class PolylineData implements Serializable {
Point2D last = points.get(points.size() - 1);
Point2D last2 = points.get(points.size() - 2);
double oldDist = last.distance(last2);
- if (oldDist <= distToTrim) {
+ if (distToTrim < 0 && oldDist <= Configuration.EPSILON) {
+ logger.debug("Cannot extend empty line");
+ last.setLocation(last2);
+ } else if (oldDist <= distToTrim) {
last.setLocation(last2);
} else {
double newDistr = oldDist - distToTrim;
diff --git a/model/src/test/java/lcsb/mapviewer/model/graphics/PolylineDataTest.java b/model/src/test/java/lcsb/mapviewer/model/graphics/PolylineDataTest.java
index 2acb342d6c10b97235f1ea55c2bc7497e4e1f632..14f57c8d638ecb2c795c76ca17e7afbc97bdeec7 100644
--- a/model/src/test/java/lcsb/mapviewer/model/graphics/PolylineDataTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/graphics/PolylineDataTest.java
@@ -14,6 +14,7 @@ import java.util.ArrayList;
import java.util.List;
import org.apache.commons.lang3.SerializationUtils;
+import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
@@ -21,401 +22,439 @@ import org.junit.Test;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.common.geometry.PointTransformation;
public class PolylineDataTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor() throws Exception {
- try {
- PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
- assertNotNull(pd);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() throws Exception {
- try {
- PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
- PolylineData pd2 = new PolylineData(pd);
- assertNotNull(pd2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor3() throws Exception {
- try {
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(1, 1));
- points.add(new Point2D.Double(5, 1));
- points.add(new Point2D.Double(5, 5));
- PolylineData pd2 = new PolylineData(points);
- assertNotNull(pd2);
- assertEquals(points.size(), pd2.getPoints().size());
- assertEquals(8, pd2.length(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddPoint() throws Exception {
- try {
- PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
- pd.addPoint(0, new Point2D.Double(-10, -10));
- assertEquals(3, pd.getPoints().size());
- assertTrue(pd.getPoints().get(0).getX() < 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddInvalidPoint() throws Exception {
- try {
- PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
- pd.addPoint(0, new Point2D.Double(Double.NEGATIVE_INFINITY, -10));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetPoint() throws Exception {
- try {
- PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
- pd.setPoint(0, new Point2D.Double(-10, -10));
- assertEquals(2, pd.getPoints().size());
- assertTrue(pd.getPoints().get(0).getX() < 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetInvalidPoint() throws Exception {
- try {
- PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
- pd.setPoint(0, new Point2D.Double(Double.NEGATIVE_INFINITY, -10));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetLines() throws Exception {
- try {
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(1, 1));
- points.add(new Point2D.Double(5, 1));
- points.add(new Point2D.Double(5, 5));
- PolylineData pd2 = new PolylineData(points);
- assertEquals(2, pd2.getLines().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvaliArgument() throws Exception {
- try {
- new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, Double.NaN));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new PolylineData());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSubline() throws Exception {
- try {
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(1, 1));
- points.add(new Point2D.Double(5, 1));
- points.add(new Point2D.Double(5, 5));
- PolylineData pd = new PolylineData(points);
- PolylineData pd2 = pd.getSubline(0, 2);
- assertNotNull(pd2);
- assertEquals(2, pd2.getPoints().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetEndPoint() throws Exception {
- try {
- PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
- pd.setEndPoint(new Point2D.Double(-10, -10));
- assertEquals(2, pd.getPoints().size());
- assertTrue(pd.getEndPoint().getX() < 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetInvalidEndPoint() throws Exception {
- try {
- PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
- pd.setEndPoint(new Point2D.Double(Double.NEGATIVE_INFINITY, -10));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetStartPoint() throws Exception {
- try {
- PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
- pd.setStartPoint(new Point2D.Double(-10, -10));
- assertEquals(2, pd.getPoints().size());
- assertTrue(pd.getBeginPoint().getX() < 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetInvalidStartPoint() throws Exception {
- try {
- PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
- pd.setStartPoint(new Point2D.Double(Double.NEGATIVE_INFINITY, -10));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToGeneralPath() throws Exception {
- try {
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(1, 1));
- points.add(new Point2D.Double(5, 1));
- points.add(new Point2D.Double(5, 5));
- PolylineData pd = new PolylineData(points);
- GeneralPath gp = pd.toGeneralPath();
- PathIterator pi = gp.getPathIterator(new AffineTransform());
- int count = 0;
- while (!pi.isDone()) {
- count++;
- pi.next();
- }
- assertEquals(3, count);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTrimEnd() throws Exception {
- try {
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(1, 1));
- points.add(new Point2D.Double(11, 1));
- PolylineData pd = new PolylineData(points);
- pd.trimEnd(3);
-
- assertEquals(8, pd.getEndPoint().getX(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTrimBegin() throws Exception {
- try {
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(1, 1));
- points.add(new Point2D.Double(11, 1));
- PolylineData pd = new PolylineData(points);
- pd.trimBegin(3);
-
- assertEquals(4, pd.getPoints().get(0).getX(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTrimEnd2() throws Exception {
- try {
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(1, 1));
- points.add(new Point2D.Double(11, 1));
- PolylineData pd = new PolylineData(points);
- pd.trimEnd(30);
-
- assertEquals(1, pd.getEndPoint().getX(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTrimBegin2() throws Exception {
- try {
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(1, 1));
- points.add(new Point2D.Double(11, 1));
- PolylineData pd = new PolylineData(points);
- pd.trimBegin(30);
-
- assertEquals(11, pd.getPoints().get(0).getX(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReverse() throws Exception {
- try {
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(1, 1));
- points.add(new Point2D.Double(11, 1));
- PolylineData pd = new PolylineData(points);
- PolylineData pd2 = pd.reverse();
- assertTrue(pd.getBeginPoint().distance(pd2.getEndPoint()) <= Configuration.EPSILON);
- assertTrue(pd2.getBeginPoint().distance(pd.getEndPoint()) <= Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testEmptyLength() throws Exception {
- try {
- PolylineData pd = new PolylineData();
- pd.addPoint(new Point2D.Double(0, 0));
- assertEquals(0, pd.length(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetInvalidPoints() throws Exception {
- try {
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(Double.NEGATIVE_INFINITY, -10));
- PolylineData pd = new PolylineData();
- pd.setPoints(points);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() throws Exception {
- try {
- PolylineData pd = new PolylineData();
- Color color = Color.BLACK;
- LineType type = LineType.DASH_DOT;
- String strWidth = "12";
- double width = 12.0;
- int id = 3;
- pd.setColor(color);
- pd.setId(id);
- pd.setType(type);
- pd.setWidth(strWidth);
-
- assertEquals(id, pd.getId());
- assertEquals(color, pd.getColor());
- assertEquals(width, pd.getWidth(), Configuration.EPSILON);
- assertEquals(type, pd.getType());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSimpleCopy() throws Exception {
- try {
- PolylineData pd = new PolylineData();
- PolylineData pd2 = pd.copy();
-
- assertNotNull(pd2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() throws Exception {
- try {
- PolylineData pd = new PolylineData() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- };
- pd.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Logger logger = Logger.getLogger(PolylineDataTest.class);
+
+ PointTransformation pr = new PointTransformation();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor() throws Exception {
+ try {
+ PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
+ assertNotNull(pd);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() throws Exception {
+ try {
+ PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
+ PolylineData pd2 = new PolylineData(pd);
+ assertNotNull(pd2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor3() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 1));
+ points.add(new Point2D.Double(5, 1));
+ points.add(new Point2D.Double(5, 5));
+ PolylineData pd2 = new PolylineData(points);
+ assertNotNull(pd2);
+ assertEquals(points.size(), pd2.getPoints().size());
+ assertEquals(8, pd2.length(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddPoint() throws Exception {
+ try {
+ PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
+ pd.addPoint(0, new Point2D.Double(-10, -10));
+ assertEquals(3, pd.getPoints().size());
+ assertTrue(pd.getPoints().get(0).getX() < 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddInvalidPoint() throws Exception {
+ try {
+ PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
+ pd.addPoint(0, new Point2D.Double(Double.NEGATIVE_INFINITY, -10));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetPoint() throws Exception {
+ try {
+ PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
+ pd.setPoint(0, new Point2D.Double(-10, -10));
+ assertEquals(2, pd.getPoints().size());
+ assertTrue(pd.getPoints().get(0).getX() < 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetInvalidPoint() throws Exception {
+ try {
+ PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
+ pd.setPoint(0, new Point2D.Double(Double.NEGATIVE_INFINITY, -10));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetLines() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 1));
+ points.add(new Point2D.Double(5, 1));
+ points.add(new Point2D.Double(5, 5));
+ PolylineData pd2 = new PolylineData(points);
+ assertEquals(2, pd2.getLines().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvaliArgument() throws Exception {
+ try {
+ new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, Double.NaN));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new PolylineData());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSubline() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 1));
+ points.add(new Point2D.Double(5, 1));
+ points.add(new Point2D.Double(5, 5));
+ PolylineData pd = new PolylineData(points);
+ PolylineData pd2 = pd.getSubline(0, 2);
+ assertNotNull(pd2);
+ assertEquals(2, pd2.getPoints().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetEndPoint() throws Exception {
+ try {
+ PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
+ pd.setEndPoint(new Point2D.Double(-10, -10));
+ assertEquals(2, pd.getPoints().size());
+ assertTrue(pd.getEndPoint().getX() < 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetInvalidEndPoint() throws Exception {
+ try {
+ PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
+ pd.setEndPoint(new Point2D.Double(Double.NEGATIVE_INFINITY, -10));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetStartPoint() throws Exception {
+ try {
+ PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
+ pd.setStartPoint(new Point2D.Double(-10, -10));
+ assertEquals(2, pd.getPoints().size());
+ assertTrue(pd.getBeginPoint().getX() < 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetInvalidStartPoint() throws Exception {
+ try {
+ PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
+ pd.setStartPoint(new Point2D.Double(Double.NEGATIVE_INFINITY, -10));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToGeneralPath() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 1));
+ points.add(new Point2D.Double(5, 1));
+ points.add(new Point2D.Double(5, 5));
+ PolylineData pd = new PolylineData(points);
+ GeneralPath gp = pd.toGeneralPath();
+ PathIterator pi = gp.getPathIterator(new AffineTransform());
+ int count = 0;
+ while (!pi.isDone()) {
+ count++;
+ pi.next();
+ }
+ assertEquals(3, count);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTrimEnd() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 1));
+ points.add(new Point2D.Double(11, 1));
+ PolylineData pd = new PolylineData(points);
+ pd.trimEnd(3);
+
+ assertEquals(8, pd.getEndPoint().getX(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTrimEndByNegativeValueOnEmptySegment() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 1));
+ points.add(new Point2D.Double(1, 1));
+ PolylineData pd = new PolylineData(points);
+ pd.trimEnd(-3);
+ for (Point2D point : pd.getPoints()) {
+ assertTrue(pr.isValidPoint(point));
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTrimEndByNegativeValue() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 1));
+ points.add(new Point2D.Double(10, 1));
+ PolylineData pd = new PolylineData(points);
+ pd.trimEnd(-3);
+ for (Point2D point : pd.getPoints()) {
+ assertTrue(pr.isValidPoint(point));
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTrimBegin() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 1));
+ points.add(new Point2D.Double(11, 1));
+ PolylineData pd = new PolylineData(points);
+ pd.trimBegin(3);
+
+ assertEquals(4, pd.getPoints().get(0).getX(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTrimEnd2() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 1));
+ points.add(new Point2D.Double(11, 1));
+ PolylineData pd = new PolylineData(points);
+ pd.trimEnd(30);
+
+ assertEquals(1, pd.getEndPoint().getX(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTrimBegin2() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 1));
+ points.add(new Point2D.Double(11, 1));
+ PolylineData pd = new PolylineData(points);
+ pd.trimBegin(30);
+
+ assertEquals(11, pd.getPoints().get(0).getX(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReverse() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 1));
+ points.add(new Point2D.Double(11, 1));
+ PolylineData pd = new PolylineData(points);
+ PolylineData pd2 = pd.reverse();
+ assertTrue(pd.getBeginPoint().distance(pd2.getEndPoint()) <= Configuration.EPSILON);
+ assertTrue(pd2.getBeginPoint().distance(pd.getEndPoint()) <= Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testEmptyLength() throws Exception {
+ try {
+ PolylineData pd = new PolylineData();
+ pd.addPoint(new Point2D.Double(0, 0));
+ assertEquals(0, pd.length(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetInvalidPoints() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(Double.NEGATIVE_INFINITY, -10));
+ PolylineData pd = new PolylineData();
+ pd.setPoints(points);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() throws Exception {
+ try {
+ PolylineData pd = new PolylineData();
+ Color color = Color.BLACK;
+ LineType type = LineType.DASH_DOT;
+ String strWidth = "12";
+ double width = 12.0;
+ int id = 3;
+ pd.setColor(color);
+ pd.setId(id);
+ pd.setType(type);
+ pd.setWidth(strWidth);
+
+ assertEquals(id, pd.getId());
+ assertEquals(color, pd.getColor());
+ assertEquals(width, pd.getWidth(), Configuration.EPSILON);
+ assertEquals(type, pd.getType());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSimpleCopy() throws Exception {
+ try {
+ PolylineData pd = new PolylineData();
+ PolylineData pd2 = pd.copy();
+
+ assertNotNull(pd2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() throws Exception {
+ try {
+ PolylineData pd = new PolylineData() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ };
+ pd.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java b/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java
index 0433a052a5f893b1410d9c166b92f436c4260da1..4fb92cf8f2349b3ab713bc69299f3ea8aa53873d 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java
@@ -90,7 +90,7 @@ public class ConvertController extends BaseController {
public Map<String, Object> getInformationImage(
@CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, ObjectNotFoundException
- {
+ {
return convertController.getInformationImage(token);
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java
index 195a8d73a56c803e0253ebcd57f1a73c9e012b71..2b29e95d8e015f4411f93dea2bdf25390f37b6a5 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java
@@ -154,6 +154,45 @@ public class ConvertRestImplTest extends RestTestFunctions {
}
}
+ @Test
+ public void testCellDesigner2Sbml2Svg() throws Exception {
+ try {
+ File file = new File("testFiles/convert/neuron_cd.xml");
+ String content = FileUtils.readFileToString(file);
+ String resultSbml = convertRestImpl.convert(token, "CellDesigner_SBML", "SBML", content).toString();
+ String resultSvg = convertRestImpl.converToImage(token, "SBML", "svg", resultSbml).toString();
+
+ // FileOutputStream outputStream = new FileOutputStream("sample-cd.png");
+ // outputStream.write(convertRestImpl.converToImage(token, "CellDesigner_SBML", "png", content).toByteArray());
+ // outputStream.close();
+
+ assertTrue(resultSvg.contains("<rect"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCellDesigner2Sbml2CellDesignerSvg() throws Exception {
+ try {
+ File file = new File("testFiles/convert/neuron_cd.xml");
+ String content = FileUtils.readFileToString(file);
+ String resultSbml = convertRestImpl.convert(token, "CellDesigner_SBML", "SBML", content).toString();
+ String resultCellDesignerSbml = convertRestImpl.convert(token, "SBML", "CellDesigner_SBML", resultSbml).toString();
+ String resultSvg = convertRestImpl.converToImage(token, "CellDesigner_SBML", "svg", resultCellDesignerSbml).toString();
+
+ // FileOutputStream outputStream = new FileOutputStream("sample-cd.png");
+ // outputStream.write(convertRestImpl.converToImage(token, "CellDesigner_SBML", "png", content).toByteArray());
+ // outputStream.close();
+
+ assertTrue(resultSvg.contains("<rect"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testScaling() throws Exception {
try {
diff --git a/rest-api/testFiles/convert/neuron_cd.xml b/rest-api/testFiles/convert/neuron_cd.xml
new file mode 100644
index 0000000000000000000000000000000000000000..895c90cd888a87114626134c6224f4dbaf4b97f6
--- /dev/null
+++ b/rest-api/testFiles/convert/neuron_cd.xml
@@ -0,0 +1,16980 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="A_comprehensive_Parkinsons_disease_map" id="A_comprehensive_Parkinsons_disease_map">
+<listOfUnitDefinitions>
+<unitDefinition id="substance" name="substance" >
+<listOfUnits>
+<unit kind="mole" scale="0" exponent="1" multiplier="1.0" />
+</listOfUnits>
+</unitDefinition><unitDefinition id="volume" name="volume" >
+<listOfUnits>
+<unit kind="litre" scale="0" exponent="1" multiplier="1.0" />
+</listOfUnits>
+</unitDefinition><unitDefinition id="area" name="area" >
+<listOfUnits>
+<unit kind="metre" scale="0" exponent="2" multiplier="1.0" />
+</listOfUnits>
+</unitDefinition><unitDefinition id="length" name="length" >
+<listOfUnits>
+<unit kind="metre" scale="0" exponent="1" multiplier="1.0" />
+</listOfUnits>
+</unitDefinition><unitDefinition id="time" name="time" >
+<listOfUnits>
+<unit kind="second" scale="0" exponent="1" multiplier="1.0" />
+</listOfUnits>
+</unitDefinition></listOfUnitDefinitions>
+<listOfFunctionDefinitions>
+</listOfFunctionDefinitions>
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="28928" sizeY="13893"/>
+<celldesigner:listOfIncludedSpecies>
+<celldesigner:species id="s_id_sa11936" name="PP2B"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1914</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11936</celldesigner:proteinReference>
+<celldesigner:name>PP2B</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11929" name="MAPK3"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1910</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11929</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+<celldesigner:modification residue="rs1" state="phosphorylated"> </celldesigner:modification>
+<celldesigner:modification residue="rs2" state="phosphorylated"> </celldesigner:modification>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>MAPK3</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11930" name="MAPK1"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1910</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11930</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+<celldesigner:modification residue="rs1" state="phosphorylated"> </celldesigner:modification>
+<celldesigner:modification residue="rs2" state="phosphorylated"> </celldesigner:modification>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>MAPK1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11961" name="PP2B"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>SemanticZoomLevelVisibility: 5
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1935</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11961</celldesigner:proteinReference>
+<celldesigner:name>PP2B</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
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+Name: glutamate ionotropic receptor AMPA type subunit 3
+Previous Symbols: GLUR3
+Synonyms: GLURC, GluA3, MRX94
+HGNC_ID: 4573
+EntrezGene_ID: 2892
+RefSeq_ID: NM_000828
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
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+</rdf:Bag>
+</bqbiol:isDescribedBy>
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+</rdf:RDF>
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+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1900</celldesigner:complexSpecies>
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+<celldesigner:proteinReference>p_s_id_sa11908</celldesigner:proteinReference>
+<celldesigner:name>GRIA3</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11909" name="GRIA1"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: GRIA1
+Name: glutamate ionotropic receptor AMPA type subunit 1
+Previous Symbols: GLUR1
+Synonyms: GLURA, GluA1
+HGNC_ID: 4571
+EntrezGene_ID: 2890
+RefSeq_ID: NM_000827
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
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+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:4571"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
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+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1900</celldesigner:complexSpecies>
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+<celldesigner:proteinReference>p_s_id_sa11909</celldesigner:proteinReference>
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+<celldesigner:listOfModifications>
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+<celldesigner:name>GRIA1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11910" name="GRIA2"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: GRIA2
+Name: glutamate ionotropic receptor AMPA type subunit 2
+Previous Symbols: GLUR2
+Synonyms: GLURB, GluA2
+HGNC_ID: 4572
+EntrezGene_ID: 2891
+RefSeq_ID: NM_000826
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+
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+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
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+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1900</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11910</celldesigner:proteinReference>
+<celldesigner:name>GRIA2</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11889" name="CASP8_space_(p18)"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: CASP8
+Name: caspase 8
+Synonyms: Casp-8, FLICE, MACH, MCH5
+HGNC_ID: 1509
+EntrezGene_ID: 841
+RefSeq_ID: NM_001228
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
+
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+<rdf:Description rdf:about="#">
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+<rdf:Bag>
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+</rdf:Bag>
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+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:CASP8"/>
+</rdf:Bag>
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+</rdf:Bag>
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+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000064012"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
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+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1890</celldesigner:complexSpecies>
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+<celldesigner:proteinReference>p_s_id_sa11889</celldesigner:proteinReference>
+<celldesigner:name>CASP8_space_(p18)</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11890" name="CASP8_space_(p10)"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: CASP8
+Name: caspase 8
+Synonyms: Casp-8, FLICE, MACH, MCH5
+HGNC_ID: 1509
+EntrezGene_ID: 841
+RefSeq_ID: NM_001228
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
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+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:1509"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:CASP8"/>
+</rdf:Bag>
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+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:Q14790"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:841"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_001228"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000064012"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1890</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11890</celldesigner:proteinReference>
+<celldesigner:name>CASP8_space_(p10)</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11903" name="HTT"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: HTT
+Name: huntingtin
+Previous Symbols: HD
+Synonyms: IT15
+HGNC_ID: 4851
+EntrezGene_ID: 3064
+RefSeq_ID: NM_002111
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:P42858"/>
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+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000197386"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:HTT"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1897</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11903</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfStructuralStates>
+<celldesigner:structuralState structuralState="mutated polyQ">mutated polyQ</celldesigner:structuralState></celldesigner:listOfStructuralStates>
+</celldesigner:state>
+<celldesigner:name>HTT</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11904" name="CTNNB1"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: CTNNB1
+Name: catenin beta 1
+Previous Symbols: CTNNB
+Synonyms: armadillo, beta-catenin
+HGNC_ID: 2514
+EntrezGene_ID: 1499
+RefSeq_ID: NM_001098210
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:CTNNB1"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
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+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:2514"/>
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+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_001098210"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
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+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:P35222"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:1499"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1897</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11904</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>CTNNB1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11884" name="PRKACA"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: PRKACA
+Name: protein kinase cAMP-activated catalytic subunit alpha
+Synonyms: PKACa
+HGNC_ID: 9380
+EntrezGene_ID: 5566
+RefSeq_ID: NM_002730
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
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+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_002730"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
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+<rdf:li rdf:resource="urn:miriam:hgnc:9380"/>
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+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:PRKACA"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:5566"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1945</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11884</celldesigner:proteinReference>
+<celldesigner:name>PRKACA</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11885" name="PRKACB"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: PRKACB
+Name: protein kinase cAMP-activated catalytic subunit beta
+Synonyms: PKACb
+HGNC_ID: 9381
+EntrezGene_ID: 5567
+RefSeq_ID: NM_182948
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000142875"/>
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+<bqbiol:isDescribedBy>
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+<rdf:li rdf:resource="urn:miriam:uniprot:P22694"/>
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+</bqbiol:isDescribedBy>
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+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:9381"/>
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+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:PRKACB"/>
+</rdf:Bag>
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+</bqbiol:isDescribedBy>
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+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1945</celldesigner:complexSpecies>
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+<celldesigner:name>PRKACB</celldesigner:name>
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+</celldesigner:species>
+<celldesigner:species id="s_id_sa11886" name="PRKACG"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: PRKACG
+Name: protein kinase cAMP-activated catalytic subunit gamma
+Synonyms: PKACg
+HGNC_ID: 9382
+EntrezGene_ID: 5568
+RefSeq_ID: NM_002732
+SemanticZoomLevelVisibility: 4
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+<celldesigner:proteinReference>p_s_id_sa11886</celldesigner:proteinReference>
+<celldesigner:name>PRKACG</celldesigner:name>
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+<celldesigner:species id="s_id_csa1947" name="catalytic_BR_subunit"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 4
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1904</celldesigner:complexSpecies>
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+<celldesigner:name>catalytic_BR_subunit</celldesigner:name>
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+TransparencyZoomLevelVisibility: 4
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1904</celldesigner:complexSpecies>
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+<celldesigner:name>regulatory_BR_subunit</celldesigner:name>
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+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11887" name="AHCYL1"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: AHCYL1
+Name: adenosylhomocysteinase like 1
+Synonyms: IRBIT, PPP1R78, XPVKONA
+HGNC_ID: 344
+EntrezGene_ID: 10768
+RefSeq_ID: NM_001242673
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
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+<rdf:Bag>
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+</rdf:Bag>
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+<celldesigner:name>AHCYL1</celldesigner:name>
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+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11888" name="VIM"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: VIM
+Name: vimentin
+HGNC_ID: 12692
+EntrezGene_ID: 7431
+RefSeq_ID: NM_003380
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
+
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+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1889</celldesigner:complexSpecies>
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+<celldesigner:state>
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+<celldesigner:modification residue="rs1" state="phosphorylated"> </celldesigner:modification>
+<celldesigner:modification residue="rs2" state="phosphorylated"> </celldesigner:modification>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>VIM</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11905" name="CFL1"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: CFL1
+Name: cofilin 1
+Previous Symbols: CFL
+HGNC_ID: 1874
+EntrezGene_ID: 1072
+RefSeq_ID: NM_005507
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
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+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
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+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
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+<celldesigner:state>
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+</celldesigner:state>
+<celldesigner:name>CFL1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11906" name="CFL2"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: CFL2
+Name: cofilin 2
+Synonyms: NEM7
+HGNC_ID: 1875
+EntrezGene_ID: 1073
+RefSeq_ID: NM_138638
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
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+<rdf:Bag>
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+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_138638"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
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+<celldesigner:complexSpecies>s_id_csa1899</celldesigner:complexSpecies>
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+<celldesigner:proteinReference>p_s_id_sa11906</celldesigner:proteinReference>
+<celldesigner:state>
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+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>CFL2</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11898" name="AHCYL1"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: AHCYL1
+Name: adenosylhomocysteinase like 1
+Synonyms: IRBIT, PPP1R78, XPVKONA
+HGNC_ID: 344
+EntrezGene_ID: 10768
+RefSeq_ID: NM_001242673
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
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+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000168710"/>
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+</rdf:Bag>
+</bqbiol:isDescribedBy>
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+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:10768"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:AHCYL1"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
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+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:344"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
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+<celldesigner:complexSpecies>s_id_csa1895</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11898</celldesigner:proteinReference>
+<celldesigner:name>AHCYL1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11899" name="ITPR3"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: ITPR3
+Name: inositol 1,4,5-trisphosphate receptor type 3
+Synonyms: IP3R3
+HGNC_ID: 6182
+EntrezGene_ID: 3710
+RefSeq_ID: NM_002224
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
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+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_002224"/>
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+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:ITPR3"/>
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+<rdf:li rdf:resource="urn:miriam:uniprot:Q14573"/>
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+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000096433"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
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+<celldesigner:complexSpecies>s_id_csa1895</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11899</celldesigner:proteinReference>
+<celldesigner:name>ITPR3</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11925" name="GRIA1"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: GRIA1
+Name: glutamate ionotropic receptor AMPA type subunit 1
+Previous Symbols: GLUR1
+Synonyms: GLURA, GluA1
+HGNC_ID: 4571
+EntrezGene_ID: 2890
+RefSeq_ID: NM_000827
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
+
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+<rdf:Description rdf:about="#">
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+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:GRIA1"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_000827"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000155511"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:2890"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:4571"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1907</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11925</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+<celldesigner:modification residue="rs1" state="phosphorylated"> </celldesigner:modification>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>GRIA1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11926" name="GRIA2"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: GRIA2
+Name: glutamate ionotropic receptor AMPA type subunit 2
+Previous Symbols: GLUR2
+Synonyms: GLURB, GluA2
+HGNC_ID: 4572
+EntrezGene_ID: 2891
+RefSeq_ID: NM_000826
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
+
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+<rdf:Description rdf:about="#">
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+<rdf:li rdf:resource="urn:miriam:uniprot:P42262"/>
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+</bqbiol:isDescribedBy>
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+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:GRIA2"/>
+</rdf:Bag>
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+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:2891"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1907</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11926</celldesigner:proteinReference>
+<celldesigner:name>GRIA2</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11927" name="GRIA4"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: GRIA4
+Name: glutamate ionotropic receptor AMPA type subunit 4
+Previous Symbols: GLUR4
+Synonyms: GLURD, GluA4
+HGNC_ID: 4574
+EntrezGene_ID: 2893
+RefSeq_ID: NM_000829
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:4574"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
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+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:GRIA4"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_000829"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:P48058"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:2893"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1907</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11927</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+<celldesigner:modification residue="rs1" state="phosphorylated"> </celldesigner:modification>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>GRIA4</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11928" name="GRIA3"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: GRIA3
+Name: glutamate ionotropic receptor AMPA type subunit 3
+Previous Symbols: GLUR3
+Synonyms: GLURC, GluA3, MRX94
+HGNC_ID: 4573
+EntrezGene_ID: 2892
+RefSeq_ID: NM_000828
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:4573"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:GRIA3"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000125675"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_000828"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:2892"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:P42263"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1907</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11928</celldesigner:proteinReference>
+<celldesigner:name>GRIA3</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11911" name="HTT"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: HTT
+Name: huntingtin
+Previous Symbols: HD
+Synonyms: IT15
+HGNC_ID: 4851
+EntrezGene_ID: 3064
+RefSeq_ID: NM_002111
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:P42858"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:4851"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:3064"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_002111"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000197386"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:HTT"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1902</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11911</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfStructuralStates>
+<celldesigner:structuralState structuralState="mutated polyQ">mutated polyQ</celldesigner:structuralState></celldesigner:listOfStructuralStates>
+</celldesigner:state>
+<celldesigner:name>HTT</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11938" name="RAP1GAP2"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: RAP1GAP2
+Name: RAP1 GTPase activating protein 2
+Previous Symbols: GARNL4
+Synonyms: KIAA1039
+HGNC_ID: 29176
+EntrezGene_ID: 23108
+RefSeq_ID: NM_015085
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000132359"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:RAP1GAP2"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:Q684P5"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:23108"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_015085"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:29176"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1917</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11938</celldesigner:proteinReference>
+<celldesigner:name>RAP1GAP2</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11939" name="RAP1GAP"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: RAP1GAP
+Name: RAP1 GTPase activating protein
+Previous Symbols: RAP1GA1
+Synonyms: KIAA0474, RAP1GAP1, RAP1GAPII
+HGNC_ID: 9858
+EntrezGene_ID: 5909
+RefSeq_ID: NM_002885
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_002885"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:RAP1GAP"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:P47736"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:9858"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000076864"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:5909"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1917</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11939</celldesigner:proteinReference>
+<celldesigner:name>RAP1GAP</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11931" name="PPP2CA"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1911</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11931</celldesigner:proteinReference>
+<celldesigner:name>PPP2CA</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11932" name="PPP2CB"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1911</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11932</celldesigner:proteinReference>
+<celldesigner:name>PPP2CB</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s_id_sa11945" name="KCNN2"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: KCNN2
+Name: potassium calcium-activated channel subfamily N member 2
+Synonyms: KCa2.2, hSK2
+HGNC_ID: 6291
+EntrezGene_ID: 3781
+RefSeq_ID: NM_021614
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000080709"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:3781"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:6291"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:Q9H2S1"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:KCNN2"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_021614"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
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+Name: potassium calcium-activated channel subfamily N member 1
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+RefSeq_ID: NM_002248
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+Name: potassium calcium-activated channel subfamily N member 3
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+Name: protein kinase cAMP-activated catalytic subunit beta
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+HGNC_ID: 9381
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+Name: protein kinase cAMP-activated catalytic subunit gamma
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+Name: cofilin 1
+Previous Symbols: CFL
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+</body></html></notes>
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+TransparencyZoomLevelVisibility: 5
+
+</body></html></notes>
+</compartment>
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+TransparencyZoomLevelVisibility: 6
+
+</body></html></notes>
+</compartment>
+<compartment metaid="s_id_ca187" id="s_id_ca187" name="ER" size="1" units="volume" outside="default" >
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+TransparencyZoomLevelVisibility: 7
+
+</body></html></notes>
+</compartment>
+<compartment metaid="default" id="default" name="" size="1" units="volume" >
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+</body></html></notes>
+</compartment>
+</listOfCompartments>
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+<celldesigner:name>Ca2_plus_</celldesigner:name>
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+<rdf:Description rdf:about="#">
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+</rdf:RDF>
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+Synonyms: 3', 5'-Cyclic AMP, adenosine 3', 5'-cyclic monophosphate, Adenosine 3', 5'-cyclic phosphate, Adenosine 3', 5'-phosphate, ADENOSINE-3', 5'-CYCLIC-MONOPHOSPHATE, cAMP, Cyclic adenylic acid, Cyclic AMP, Recon metabolite: camp
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+VMH database: <a href="http://vmh.uni.lu/#metabolite/camp">camp</a></body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
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+Name: beta-transducin repeat containing E3 ubiquitin protein ligase
+Synonyms: FBXW1A, Fwd1, bTrCP, bTrCP1, beta-TrCP1, betaTrCP
+HGNC_ID: 1144
+EntrezGene_ID: 8945
+RefSeq_ID: NM_033637
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
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+<celldesigner:proteinReference>p_s_id_sa11843</celldesigner:proteinReference>
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+<rdf:Description rdf:about="#">
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+<celldesigner:proteinReference>p_s_id_sa11790</celldesigner:proteinReference>
+<celldesigner:name>HTR6</celldesigner:name>
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+<rdf:Description rdf:about="#">
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+<species name="PP1" id="s_id_csa1941" metaid="s_id_csa1941" initialAmount="0.0" compartment="s_id_ca188"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>PP1</celldesigner:name>
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+<rdf:Description rdf:about="#">
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+<celldesigner:proteinReference>p_s_id_sa11772</celldesigner:proteinReference>
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+<rdf:Description rdf:about="#">
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+</annotation>
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+<species name="GABA" id="s_id_sa11776" metaid="s_id_sa11776" initialAmount="0.0" charge="0" compartment="s_id_ca183"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>GABA</celldesigner:name>
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+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
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+<rdf:Bag>
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+</rdf:RDF>
+</annotation>
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+<species name="Phospholipase_space_C" id="s_id_sa11734" metaid="s_id_sa11734" initialAmount="0.0" compartment="s_id_ca188"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11734</celldesigner:proteinReference>
+<celldesigner:name>Phospholipase_space_C</celldesigner:name>
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+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:hasPart>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:interpro:IPR001192"/>
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+</rdf:RDF>
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+<celldesigner:proteinReference>p_s_id_sa11783</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
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+<celldesigner:name>PTPN5</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="Calcineurin" id="s_id_csa1914" metaid="s_id_csa1914" initialAmount="0.0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>Calcineurin</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0004723"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:mesh:D019703"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="cAMP" id="s_id_sa11703" metaid="s_id_sa11703" initialAmount="0.0" charge="0" compartment="s_id_ca173"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Name: 3',5'-cyclic AMP
+Synonyms: 3', 5'-Cyclic AMP, adenosine 3', 5'-cyclic monophosphate, Adenosine 3', 5'-cyclic phosphate, Adenosine 3', 5'-phosphate, ADENOSINE-3', 5'-CYCLIC-MONOPHOSPHATE, cAMP, Cyclic adenylic acid, Cyclic AMP, Recon metabolite: camp
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+VMH database: <a href="http://vmh.uni.lu/#metabolite/camp">camp</a></body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>cAMP</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A17489"/>
+</rdf:Bag>
+</bqbiol:is>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="ERK1_slash_2" id="s_id_csa1910" metaid="s_id_csa1910" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>ERK1_slash_2</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:interpro:IPR008349"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="cellular_space_calcium" id="s_id_sa11770" metaid="s_id_sa11770" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PHENOTYPE</celldesigner:class>
+<celldesigner:name>cellular_space_calcium</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0006874"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="Calcineurin" id="s_id_csa1935" metaid="s_id_csa1935" initialAmount="0.0" compartment="s_id_ca182"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>Calcineurin</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0004723"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:mesh:D019703"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="RANBP9" id="s_id_sa11754" metaid="s_id_sa11754" initialAmount="0.0" compartment="s_id_ca188"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: RANBP9
+Name: RAN binding protein 9
+Synonyms: RanBPM
+HGNC_ID: 13727
+EntrezGene_ID: 10048
+RefSeq_ID: NM_005493
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11754</celldesigner:proteinReference>
+<celldesigner:name>RANBP9</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:13727"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000010017"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:Q96S59"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_005493"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:RANBP9"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:10048"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="Ca2_plus_" id="s_id_sa11769" metaid="s_id_sa11769" initialAmount="0.0" compartment="default"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>ION</celldesigner:class>
+<celldesigner:name>Ca2_plus_</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="synaptic_space_plasticity" id="s_id_sa11810" metaid="s_id_sa11810" initialAmount="0.0" compartment="s_id_ca182"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PHENOTYPE</celldesigner:class>
+<celldesigner:name>synaptic_space_plasticity</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0031915"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="chromatin_space_organization" id="s_id_sa11799" metaid="s_id_sa11799" initialAmount="0.0" charge="0" compartment="s_id_ca182"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PHENOTYPE</celldesigner:class>
+<celldesigner:name>chromatin_space_organization</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0006325"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="EEF2K" id="s_id_sa11711" metaid="s_id_sa11711" initialAmount="0.0" charge="0" compartment="s_id_ca173"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: EEF2K
+Name: eukaryotic elongation factor 2 kinase
+Synonyms: eEF-2K
+HGNC_ID: 24615
+EntrezGene_ID: 29904
+RefSeq_ID: NM_013302
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11711</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>EEF2K</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:24615"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_013302"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:EEF2K"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:O00418"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000103319"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:29904"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PRKAR2B" id="s_id_sa11730" metaid="s_id_sa11730" initialAmount="0.0" charge="0" compartment="s_id_ca173"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: PRKAR2B
+Name: protein kinase cAMP-dependent type II regulatory subunit beta
+Previous Symbols: PRKAR2
+HGNC_ID: 9392
+EntrezGene_ID: 5577
+RefSeq_ID: NM_002736
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11730</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>PRKAR2B</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:9392"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:P31323"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000005249"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:PRKAR2B"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_002736"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:5577"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="RASGRP2" id="s_id_sa11760" metaid="s_id_sa11760" initialAmount="0.0" charge="0" compartment="s_id_ca173"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: RASGRP2
+Name: RAS guanyl releasing protein 2
+Synonyms: CALDAG-GEFI
+HGNC_ID: 9879
+EntrezGene_ID: 10235
+RefSeq_ID: NM_153819
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11760</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+<celldesigner:modification residue="rs1" state="phosphorylated"> </celldesigner:modification>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>RASGRP2</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_153819"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:RASGRP2"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:9879"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:Q7LDG7"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000068831"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:10235"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="acetylcholine" id="s_id_sa11832" metaid="s_id_sa11832" initialAmount="0.0" compartment="default"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>acetylcholine</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="Calmodulin" id="s_id_csa1916" metaid="s_id_csa1916" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>Calmodulin</celldesigner:name>
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+<rdf:Description rdf:about="#">
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+<rdf:li rdf:resource="urn:miriam:mesh:D002147"/>
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+<species name="PPP1R1B" id="s_id_sa11811" metaid="s_id_sa11811" initialAmount="0.0" compartment="s_id_ca182"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11811</celldesigner:proteinReference>
+<celldesigner:state>
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+<celldesigner:name>PPP1R1B</celldesigner:name>
+</celldesigner:speciesIdentity>
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+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
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+<species name="adenylyl_space_cyclase" id="s_id_csa1903" metaid="s_id_csa1903" initialAmount="0.0" charge="0" compartment="s_id_ca169"><annotation><celldesigner:extension><celldesigner:positionToCompartment>innerSurface</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>adenylyl_space_cyclase</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
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+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
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+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ec-code:4.6.1.1"/>
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+</rdf:RDF>
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+<species name="PP1" id="s_id_csa1928" metaid="s_id_csa1928" initialAmount="0.0" compartment="s_id_ca182"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>PP1</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+</celldesigner:speciesIdentity>
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+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:mesh:D054645"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PP1" id="s_id_csa1913" metaid="s_id_csa1913" initialAmount="0.0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>PP1</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:mesh:D054645"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="postsynaptic_space_response" id="s_id_sa11717" metaid="s_id_sa11717" initialAmount="0.0" charge="0" compartment="s_id_ca168"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Name: excitatory postsynaptic potential
+SemanticZoomLevelVisibility: 6
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+A process that leads to a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential.</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PHENOTYPE</celldesigner:class>
+<celldesigner:name>postsynaptic_space_response</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0060079"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PPP1R1B" id="s_id_sa11786" metaid="s_id_sa11786" initialAmount="0.0" compartment="s_id_ca182"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11786</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+<celldesigner:modification residue="rs2" state="phosphorylated"> </celldesigner:modification>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>PPP1R1B</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="TF_space_EGR1" id="s_id_csa1944" metaid="s_id_csa1944" initialAmount="0.0" charge="0" compartment="s_id_ca182"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>TF_space_EGR1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="RANBP9" id="s_id_sa11764" metaid="s_id_sa11764" initialAmount="0.0" charge="0" compartment="s_id_ca169"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: RANBP9
+Name: RAN binding protein 9
+Synonyms: RanBPM
+HGNC_ID: 13727
+EntrezGene_ID: 10048
+RefSeq_ID: NM_005493
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11764</celldesigner:proteinReference>
+<celldesigner:name>RANBP9</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:13727"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000010017"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:Q96S59"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_005493"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:RANBP9"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:10048"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PTPN5" id="s_id_sa11784" metaid="s_id_sa11784" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11784</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+<celldesigner:modification residue="rs1" state="phosphorylated"> </celldesigner:modification>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>PTPN5</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="EEF2K" id="s_id_sa11708" metaid="s_id_sa11708" initialAmount="0.0" charge="0" compartment="s_id_ca173"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: EEF2K
+Name: eukaryotic elongation factor 2 kinase
+Synonyms: eEF-2K
+HGNC_ID: 24615
+EntrezGene_ID: 29904
+RefSeq_ID: NM_013302
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11708</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+<celldesigner:modification residue="rs1" state="phosphorylated"> </celldesigner:modification>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>EEF2K</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:24615"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_013302"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:EEF2K"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:O00418"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000103319"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:29904"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="ARPP21" id="s_id_sa11842" metaid="s_id_sa11842" initialAmount="0.0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11842</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+<celldesigner:modification residue="rs1" state="phosphorylated"> </celldesigner:modification>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>ARPP21</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PPP1R1B" id="s_id_sa11771" metaid="s_id_sa11771" initialAmount="0.0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11771</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>PPP1R1B</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="HTT" id="s_id_sa11738" metaid="s_id_sa11738" initialAmount="0.0" charge="0" compartment="s_id_ca173"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: HTT
+Name: huntingtin
+Previous Symbols: HD
+Synonyms: IT15
+HGNC_ID: 4851
+EntrezGene_ID: 3064
+RefSeq_ID: NM_002111
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11738</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfStructuralStates>
+<celldesigner:structuralState structuralState="mutated polyQ">mutated polyQ</celldesigner:structuralState></celldesigner:listOfStructuralStates>
+</celldesigner:state>
+<celldesigner:name>HTT</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:P42858"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:4851"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:3064"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_002111"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000197386"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:HTT"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="DRD1" id="s_id_sa11750" metaid="s_id_sa11750" initialAmount="0.0" charge="0" compartment="s_id_ca169"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: DRD1
+Name: dopamine receptor D1
+HGNC_ID: 3020
+EntrezGene_ID: 1812
+RefSeq_ID: NM_000794
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11750</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+<celldesigner:modification residue="rs1" state="phosphorylated"> </celldesigner:modification>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>DRD1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:DRD1"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_000794"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:1812"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000184845"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:3020"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:P21728"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="ITGB1" id="s_id_sa11707" metaid="s_id_sa11707" initialAmount="0.0" charge="0" compartment="s_id_ca188"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: ITGB1
+Name: integrin subunit beta 1
+Previous Symbols: FNRB, MSK12, MDF2
+Synonyms: CD29, GPIIA
+HGNC_ID: 6153
+EntrezGene_ID: 3688
+RefSeq_ID: NM_002211
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11707</celldesigner:proteinReference>
+<celldesigner:name>ITGB1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_002211"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:P05556"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:ITGB1"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:3688"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:6153"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000150093"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="ROCK" id="s_id_csa1906" metaid="s_id_csa1906" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>ROCK</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isPartOf>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:interpro:IPR020684"/>
+</rdf:Bag>
+</bqbiol:isPartOf>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="AHCYL1" id="s_id_sa11757" metaid="s_id_sa11757" initialAmount="0.0" charge="0" compartment="s_id_ca173"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: AHCYL1
+Name: adenosylhomocysteinase like 1
+Synonyms: IRBIT, PPP1R78, XPVKONA
+HGNC_ID: 344
+EntrezGene_ID: 10768
+RefSeq_ID: NM_001242673
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11757</celldesigner:proteinReference>
+<celldesigner:name>AHCYL1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000168710"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:O43865"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_001242673"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:10768"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:AHCYL1"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:344"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="TF_space_CREB" id="s_id_csa1920" metaid="s_id_csa1920" initialAmount="0.0" charge="0" compartment="s_id_ca182"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>TF_space_CREB</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PKA" id="s_id_csa1931" metaid="s_id_csa1931" initialAmount="0.0" compartment="s_id_ca188"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Name: cAMP-dependent protein kinase complex
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 7
+
+An enzyme complex, composed of regulatory and catalytic subunits, that catalyzes protein phosphorylation. Inactive forms of the enzyme have two regulatory chains and two catalytic chains; activation by cAMP produces two active catalytic monomers and a regulatory dimer.</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>PKA</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0005952"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="VIM" id="s_id_sa11745" metaid="s_id_sa11745" initialAmount="0.0" charge="0" compartment="s_id_ca173"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: VIM
+Name: vimentin
+HGNC_ID: 12692
+EntrezGene_ID: 7431
+RefSeq_ID: NM_003380
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11745</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+<celldesigner:modification residue="rs1" state="phosphorylated"> </celldesigner:modification>
+<celldesigner:modification residue="rs2" state="phosphorylated"> </celldesigner:modification>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>VIM</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:7431"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_003380"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000026025"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:P08670"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:12692"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:VIM"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="CaMKII" id="s_id_csa1937" metaid="s_id_csa1937" initialAmount="0.0" compartment="s_id_ca188"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:state>
+<celldesigner:listOfStructuralStates>
+<celldesigner:structuralState structuralState="phosphorylated">phosphorylated</celldesigner:structuralState></celldesigner:listOfStructuralStates>
+</celldesigner:state>
+<celldesigner:name>CaMKII</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="Ca2_plus_" id="s_id_sa11724" metaid="s_id_sa11724" initialAmount="0.0" compartment="s_id_ca187"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>ION</celldesigner:class>
+<celldesigner:name>Ca2_plus_</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="AMPA_space_receptor" id="s_id_csa1900" metaid="s_id_csa1900" initialAmount="0.0" charge="0" compartment="s_id_ca188"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Name: AMPA glutamate receptor complex
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 4
+Charge: 0
+
+An assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex. The AMPA receptors mediate fast synaptic transmission in the CNS and are composed of subunits GluR1-4, products from separate genes. These subunits have an extracellular N-terminus and an intracellular C-terminus.</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>AMPA_space_receptor</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0032281"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="Ca2_plus_" id="s_id_sa11706" metaid="s_id_sa11706" initialAmount="0.0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>ION</celldesigner:class>
+<celldesigner:name>Ca2_plus_</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="RASGRF1" id="s_id_sa11821" metaid="s_id_sa11821" initialAmount="0.0" compartment="s_id_ca188"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11821</celldesigner:proteinReference>
+<celldesigner:name>RASGRF1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pubmed:16467520"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PINK1" id="s_id_sa11712" metaid="s_id_sa11712" initialAmount="0.0" charge="0" compartment="s_id_ca168"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: PINK1
+Name: PTEN induced putative kinase 1
+Previous Symbols: PARK6
+HGNC_ID: 14581
+EntrezGene_ID: 65018
+RefSeq_ID: NM_032409
+SemanticZoomLevelVisibility: 6
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11712</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>PINK1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:65018"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:Q9BXM7"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:PINK1"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000158828"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_032409"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:14581"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="ITPR1" id="s_id_sa11713" metaid="s_id_sa11713" initialAmount="0.0" charge="0" compartment="s_id_ca187"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: ITPR1
+Name: inositol 1,4,5-trisphosphate receptor type 1
+Previous Symbols: SCA15, SCA16, SCA29
+Synonyms: ACV, IP3R1, Insp3r1, PPP1R94
+HGNC_ID: 6180
+EntrezGene_ID: 3708
+RefSeq_ID: NM_002222
+SemanticZoomLevelVisibility: 7
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11713</celldesigner:proteinReference>
+<celldesigner:name>ITPR1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_002222"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:ITPR1"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:6180"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:3708"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000150995"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:Q14643"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="EGR1" id="s_id_sa11826" metaid="s_id_sa11826" initialAmount="0.0" charge="0" compartment="s_id_ca182"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>RNA</celldesigner:class>
+<celldesigner:rnaReference>r_s_id_sa11826</celldesigner:rnaReference>
+<celldesigner:name>EGR1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="Caspase_minus_8" id="s_id_csa1890" metaid="s_id_csa1890" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>Caspase_minus_8</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="cAMP" id="s_id_sa11795" metaid="s_id_sa11795" initialAmount="0.0" charge="0" compartment="s_id_ca188"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Name: 3',5'-cyclic AMP
+Synonyms: 3', 5'-Cyclic AMP, adenosine 3', 5'-cyclic monophosphate, Adenosine 3', 5'-cyclic phosphate, Adenosine 3', 5'-phosphate, ADENOSINE-3', 5'-CYCLIC-MONOPHOSPHATE, cAMP, Cyclic adenylic acid, Cyclic AMP, Recon metabolite: camp
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+VMH database: <a href="http://vmh.uni.lu/#metabolite/camp">camp</a></body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>cAMP</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A17489"/>
+</rdf:Bag>
+</bqbiol:is>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="K_plus_" id="s_id_sa11761" metaid="s_id_sa11761" initialAmount="0.0" compartment="default"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>ION</celldesigner:class>
+<celldesigner:name>K_plus_</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PPP1R1B" id="s_id_sa11836" metaid="s_id_sa11836" initialAmount="0.0" charge="0" compartment="s_id_ca182"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>RNA</celldesigner:class>
+<celldesigner:rnaReference>r_s_id_sa11836</celldesigner:rnaReference>
+<celldesigner:name>PPP1R1B</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="cannabinoid" id="s_id_sa11847" metaid="s_id_sa11847" initialAmount="0.0" compartment="default"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>cannabinoid</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="IP3_space_" id="s_id_sa11736" metaid="s_id_sa11736" initialAmount="0.0" compartment="s_id_ca188"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Name: 1D-myo-inositol 1,4,5-trisphosphate
+Synonyms: 1, 4, 5-Insp3, 1D-myo-Inositol 1, 4, 5-trisphosphate, D-myo-Inositol 1, 4, 5-trisphosphate, D-MYO-INOSITOL-1, 4, 5-TRIPHOSPHATE, Inositol 1, 4, 5-trisphosphate, Ins(1, 4, 5)P3, InsP3, IP3, Recon metabolite: mi145p
+SemanticZoomLevelVisibility: 6
+TransparencyZoomLevelVisibility: 0
+
+VMH database: <a href="http://vmh.uni.lu/#metabolite/mi145p">mi145p</a></body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>IP3_space_</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A16595"/>
+</rdf:Bag>
+</bqbiol:is>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PRKAR2B" id="s_id_sa11751" metaid="s_id_sa11751" initialAmount="0.0" charge="0" compartment="s_id_ca168"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: PRKAR2B
+Name: protein kinase cAMP-dependent type II regulatory subunit beta
+Previous Symbols: PRKAR2
+HGNC_ID: 9392
+EntrezGene_ID: 5577
+RefSeq_ID: NM_002736
+SemanticZoomLevelVisibility: 6
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11751</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+<celldesigner:modification residue="rs1" state="phosphorylated"> </celldesigner:modification>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>PRKAR2B</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:9392"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:P31323"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000005249"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:PRKAR2B"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_002736"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:5577"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="CTNNB1:HTT" id="s_id_csa1897" metaid="s_id_csa1897" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>CTNNB1:HTT</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="TRPV1" id="s_id_sa11794" metaid="s_id_sa11794" initialAmount="0.0" charge="0" compartment="s_id_ca188"><annotation><celldesigner:extension><celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11794</celldesigner:proteinReference>
+<celldesigner:name>TRPV1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="diglyceride" id="s_id_sa11733" metaid="s_id_sa11733" initialAmount="0.0" compartment="s_id_ca188"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Name: diglyceride
+Synonyms: a diacylglycerol, di-O-acylglycerols, Diacylglycerol, diacylglycerols, Diglyceride, diglycerides
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>innerSurface</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>diglyceride</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A18035"/>
+</rdf:Bag>
+</bqbiol:is>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="CAMK4" id="s_id_sa11857" metaid="s_id_sa11857" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11857</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>CAMK4</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="RAP1A" id="s_id_sa11808" metaid="s_id_sa11808" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11808</celldesigner:proteinReference>
+<celldesigner:name>RAP1A</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="DRD1" id="s_id_sa11696" metaid="s_id_sa11696" initialAmount="0.0" charge="0" compartment="s_id_ca169"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: DRD1
+Name: dopamine receptor D1
+HGNC_ID: 3020
+EntrezGene_ID: 1812
+RefSeq_ID: NM_000794
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11696</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>DRD1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:DRD1"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_000794"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:1812"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000184845"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:3020"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:P21728"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="degraded_space_CTNNB1" id="s_id_sa11740" metaid="s_id_sa11740" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>DEGRADED</celldesigner:class>
+<celldesigner:name>degraded_space_CTNNB1</celldesigner:name>
+</celldesigner:speciesIdentity>
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+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="Calcineurin" id="s_id_csa1904" metaid="s_id_csa1904" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>Calcineurin</celldesigner:name>
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+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
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+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0004723"/>
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+<celldesigner:name>AHCYL:ITPR3</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="UPS" id="s_id_sa11719" metaid="s_id_sa11719" initialAmount="0.0" compartment="s_id_ca173"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Name: proteasome complex
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+
+A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PHENOTYPE</celldesigner:class>
+<celldesigner:name>UPS</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqmodel:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0000502"/>
+</rdf:Bag>
+</bqmodel:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="cofilin" id="s_id_csa1899" metaid="s_id_csa1899" initialAmount="0.0" charge="0" compartment="s_id_ca169"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>cofilin</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="AMP" id="s_id_sa11844" metaid="s_id_sa11844" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>AMP</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="UPS" id="s_id_sa11732" metaid="s_id_sa11732" initialAmount="0.0" compartment="s_id_ca173"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Name: proteasome complex
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
+
+A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PHENOTYPE</celldesigner:class>
+<celldesigner:name>UPS</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqmodel:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0000502"/>
+</rdf:Bag>
+</bqmodel:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PKA" id="s_id_csa1901" metaid="s_id_csa1901" initialAmount="0.0" compartment="s_id_ca168"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Name: cAMP-dependent protein kinase complex
+SemanticZoomLevelVisibility: 6
+TransparencyZoomLevelVisibility: 7
+
+An enzyme complex, composed of regulatory and catalytic subunits, that catalyzes protein phosphorylation. Inactive forms of the enzyme have two regulatory chains and two catalytic chains; activation by cAMP produces two active catalytic monomers and a regulatory dimer.</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>PKA</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0005952"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="RASGRF1" id="s_id_sa11822" metaid="s_id_sa11822" initialAmount="0.0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11822</celldesigner:proteinReference>
+<celldesigner:name>RASGRF1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="AHCYL1:ITPR3" id="s_id_csa1895" metaid="s_id_csa1895" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>AHCYL1:ITPR3</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PENK" id="s_id_sa11858" metaid="s_id_sa11858" initialAmount="0.0" compartment="default"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11858</celldesigner:proteinReference>
+<celldesigner:name>PENK</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="LRRK2" id="s_id_sa11718" metaid="s_id_sa11718" initialAmount="0.0" compartment="s_id_ca168"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: LRRK2
+Name: leucine rich repeat kinase 2
+Previous Symbols: PARK8
+Synonyms: DKFZp434H2111, FLJ45829, RIPK7, ROCO2
+HGNC_ID: 18618
+EntrezGene_ID: 120892
+RefSeq_ID: XM_058513
+SemanticZoomLevelVisibility: 6
+TransparencyZoomLevelVisibility: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11718</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>LRRK2</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:120892"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:Q5S007"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:18618"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:XM_058513"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000188906"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:LRRK2"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="AMPA_space_receptor" id="s_id_csa1907" metaid="s_id_csa1907" initialAmount="0.0" charge="0" compartment="s_id_ca188"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Name: AMPA glutamate receptor complex
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 3
+Charge: 0
+
+An assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex. The AMPA receptors mediate fast synaptic transmission in the CNS and are composed of subunits GluR1-4, products from separate genes. These subunits have an extracellular N-terminus and an intracellular C-terminus.</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>AMPA_space_receptor</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0032281"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="L_minus_glutamate" id="s_id_sa11872" metaid="s_id_sa11872" initialAmount="0.0" charge="0" compartment="default"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Name: L-glutamic acid
+Synonyms: (S)-2-aminopentanedioic acid, (S)-glutamic acid, acide glutamique, acido glutamico, acidum glutamicum, E, Glu, Glutamate, GLUTAMIC ACID, glutamic acid, L-Glu, L-Glutamic acid, L-Glutaminic acid, L-Glutaminsaeure, Recon metabolite: glu_L
+Reactome_ID: REACT_13119.1
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+VMH database: <a href="http://vmh.uni.lu/#metabolite/glu_L">glu_L</a></body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>L_minus_glutamate</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A16015"/>
+</rdf:Bag>
+</bqbiol:is>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:reactome:REACT_13119.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="inclusion" id="s_id_csa1902" metaid="s_id_csa1902" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>inclusion</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="filamentous_space_actin" id="s_id_csa1898" metaid="s_id_csa1898" initialAmount="0.0" charge="0" compartment="s_id_ca169"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Name: filamentous actin
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 7
+Charge: 0
+
+A two-stranded helical polymer of the protein actin.</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>filamentous_space_actin</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0031941"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="LRRK2" id="s_id_sa11726" metaid="s_id_sa11726" initialAmount="0.0" charge="0" compartment="s_id_ca188"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: LRRK2
+Name: leucine rich repeat kinase 2
+Previous Symbols: PARK8
+Synonyms: DKFZp434H2111, FLJ45829, RIPK7, ROCO2
+HGNC_ID: 18618
+EntrezGene_ID: 120892
+RefSeq_ID: XM_058513
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11726</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>LRRK2</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:120892"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:Q5S007"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:18618"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:XM_058513"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000188906"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:LRRK2"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="protein_space_translation" id="s_id_sa11705" metaid="s_id_sa11705" initialAmount="0.0" charge="0" compartment="s_id_ca173"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Name: regulation of cytoplasmic translational elongation
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+Any process that modulates the frequency, rate or extent of cytoplasmic translational elongation.</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PHENOTYPE</celldesigner:class>
+<celldesigner:name>protein_space_translation</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A1900247"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="K_plus_" id="s_id_sa11721" metaid="s_id_sa11721" initialAmount="0.0" compartment="s_id_ca188"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>ION</celldesigner:class>
+<celldesigner:name>K_plus_</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="CTNNB1" id="s_id_sa11720" metaid="s_id_sa11720" initialAmount="0.0" charge="0" compartment="s_id_ca173"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: CTNNB1
+Name: catenin beta 1
+Previous Symbols: CTNNB
+Synonyms: armadillo, beta-catenin
+HGNC_ID: 2514
+EntrezGene_ID: 1499
+RefSeq_ID: NM_001098210
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11720</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>CTNNB1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:CTNNB1"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:2514"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_001098210"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000168036"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:P35222"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:1499"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="CHRM4" id="s_id_sa11831" metaid="s_id_sa11831" initialAmount="0.0" charge="0" compartment="s_id_ca188"><annotation><celldesigner:extension><celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11831</celldesigner:proteinReference>
+<celldesigner:name>CHRM4</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PKA_space_catalytic_space_subunit" id="s_id_csa1915" metaid="s_id_csa1915" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>PKA_space_catalytic_space_subunit</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ec-code:2.7.11.11"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="ARPP21" id="s_id_sa11841" metaid="s_id_sa11841" initialAmount="0.0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11841</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>ARPP21</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="dendritic_space_spine_space_development" id="s_id_sa11725" metaid="s_id_sa11725" initialAmount="0.0" charge="0" compartment="s_id_ca169"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Name: dendritic spine development
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+The process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PHENOTYPE</celldesigner:class>
+<celldesigner:name>dendritic_space_spine_space_development</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0060996"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="BTRC" id="s_id_sa11697" metaid="s_id_sa11697" initialAmount="0.0" compartment="s_id_ca173"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: BTRC
+Name: beta-transducin repeat containing E3 ubiquitin protein ligase
+Synonyms: FBXW1A, Fwd1, bTrCP, bTrCP1, beta-TrCP1, betaTrCP
+HGNC_ID: 1144
+EntrezGene_ID: 8945
+RefSeq_ID: NM_033637
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11697</celldesigner:proteinReference>
+<celldesigner:name>BTRC</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000166167"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:Q9Y297"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:1144"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:BTRC"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:8945"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_033637"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="VIM" id="s_id_sa11737" metaid="s_id_sa11737" initialAmount="0.0" charge="0" compartment="s_id_ca173"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: VIM
+Name: vimentin
+HGNC_ID: 12692
+EntrezGene_ID: 7431
+RefSeq_ID: NM_003380
+SemanticZoomLevelVisibility: 3
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11737</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>VIM</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:7431"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_003380"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000026025"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:P08670"/>
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+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:12692"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:VIM"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PRKCD" id="s_id_sa11723" metaid="s_id_sa11723" initialAmount="0.0" charge="0" compartment="s_id_ca169"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: PRKCD
+Name: protein kinase C delta
+HGNC_ID: 9399
+EntrezGene_ID: 5580
+RefSeq_ID: NM_001316327
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11723</celldesigner:proteinReference>
+<celldesigner:name>PRKCD</celldesigner:name>
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+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:PRKCD"/>
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+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:Q05655"/>
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+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000163932"/>
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+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:9399"/>
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+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_001316327"/>
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+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PPP1R1B" id="s_id_sa11779" metaid="s_id_sa11779" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11779</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+<celldesigner:modification residue="rs2" state="phosphorylated"> </celldesigner:modification>
+<celldesigner:modification residue="rs3" state="phosphorylated"> </celldesigner:modification>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>PPP1R1B</celldesigner:name>
+</celldesigner:speciesIdentity>
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+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PP2C" id="s_id_sa11834" metaid="s_id_sa11834" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11834</celldesigner:proteinReference>
+<celldesigner:name>PP2C</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
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+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:interpro:IPR015655"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="degraded_space_EEF2K" id="s_id_sa11756" metaid="s_id_sa11756" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>DEGRADED</celldesigner:class>
+<celldesigner:name>degraded_space_EEF2K</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="Rap1_space_activating" id="s_id_csa1917" metaid="s_id_csa1917" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>Rap1_space_activating</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+</celldesigner:speciesIdentity>
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+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:interpro:IPR000331"/>
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+</bqbiol:isEncodedBy>
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+</rdf:RDF>
+</annotation>
+</species>
+<species name="NTRK2" id="s_id_sa11700" metaid="s_id_sa11700" initialAmount="0.0" charge="0" compartment="s_id_ca188"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: NTRK2
+Name: neurotrophic receptor tyrosine kinase 2
+Synonyms: TRKB
+HGNC_ID: 8032
+EntrezGene_ID: 4915
+RefSeq_ID: XM_005252001
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11700</celldesigner:proteinReference>
+<celldesigner:name>NTRK2</celldesigner:name>
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+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:Q16620"/>
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+<bqbiol:isDescribedBy>
+<rdf:Bag>
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+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:4915"/>
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+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:8032"/>
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+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:NTRK2"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000148053"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="long_minus_term_space_memory" id="s_id_sa11809" metaid="s_id_sa11809" initialAmount="0.0" charge="0" compartment="s_id_ca182"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PHENOTYPE</celldesigner:class>
+<celldesigner:name>long_minus_term_space_memory</celldesigner:name>
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+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0007616"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PP2A" id="s_id_csa1911" metaid="s_id_csa1911" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>PP2A</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+</celldesigner:speciesIdentity>
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+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:mesh:D054648"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="mitochondrial_space_motility" id="s_id_sa11729" metaid="s_id_sa11729" initialAmount="0.0" charge="0" compartment="s_id_ca168"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Name: mitochondrion transport along microtubule
+SemanticZoomLevelVisibility: 6
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+The directed movement of a mitochondrion along a microtubule, mediated by motor proteins.</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PHENOTYPE</celldesigner:class>
+<celldesigner:name>mitochondrial_space_motility</celldesigner:name>
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+<rdf:Description rdf:about="#">
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+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0047497"/>
+</rdf:Bag>
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+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="Ca2_plus_" id="s_id_sa11788" metaid="s_id_sa11788" initialAmount="0.0" compartment="s_id_ca169"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>ION</celldesigner:class>
+<celldesigner:name>Ca2_plus_</celldesigner:name>
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+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="synaptic_space_plasticity" id="s_id_sa11848" metaid="s_id_sa11848" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PHENOTYPE</celldesigner:class>
+<celldesigner:name>synaptic_space_plasticity</celldesigner:name>
+</celldesigner:speciesIdentity>
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+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0031915"/>
+</rdf:Bag>
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+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="small_minus_conductance_space_KCa_space_channels" id="s_id_csa1924" metaid="s_id_csa1924" initialAmount="0.0" charge="0" compartment="s_id_ca188"><annotation><celldesigner:extension><celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>small_minus_conductance_space_KCa_space_channels</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
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+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isPartOf>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:interpro:IPR015449"/>
+</rdf:Bag>
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+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="ITPR2" id="s_id_sa11755" metaid="s_id_sa11755" initialAmount="0.0" charge="0" compartment="s_id_ca187"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: ITPR2
+Name: inositol 1,4,5-trisphosphate receptor type 2
+Synonyms: CFAP48, IP3R2
+HGNC_ID: 6181
+EntrezGene_ID: 3709
+RefSeq_ID: NM_002223
+SemanticZoomLevelVisibility: 7
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11755</celldesigner:proteinReference>
+<celldesigner:name>ITPR2</celldesigner:name>
+</celldesigner:speciesIdentity>
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+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_002223"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:Q14571"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:ITPR2"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:3709"/>
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+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:6181"/>
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+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000123104"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PP2A" id="s_id_csa1943" metaid="s_id_csa1943" initialAmount="0.0" charge="0" compartment="s_id_ca188"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>PP2A</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="RGS4" id="s_id_sa11702" metaid="s_id_sa11702" initialAmount="0.0" charge="0" compartment="s_id_ca173"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: RGS4
+Name: regulator of G-protein signaling 4
+Previous Symbols: SCZD9
+HGNC_ID: 10000
+EntrezGene_ID: 5999
+RefSeq_ID: NM_005613
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11702</celldesigner:proteinReference>
+<celldesigner:name>RGS4</celldesigner:name>
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+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_005613"/>
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+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:5999"/>
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+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
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+<rdf:li rdf:resource="urn:miriam:uniprot:P49798"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000117152"/>
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+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:10000"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:RGS4"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PDYN" id="s_id_sa11827" metaid="s_id_sa11827" initialAmount="0.0" charge="0" compartment="s_id_ca182"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>RNA</celldesigner:class>
+<celldesigner:rnaReference>r_s_id_sa11827</celldesigner:rnaReference>
+<celldesigner:name>PDYN</celldesigner:name>
+</celldesigner:speciesIdentity>
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+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="GRM1" id="s_id_sa11766" metaid="s_id_sa11766" initialAmount="0.0" charge="0" compartment="s_id_ca188"><annotation><celldesigner:extension><celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11766</celldesigner:proteinReference>
+<celldesigner:name>GRM1</celldesigner:name>
+</celldesigner:speciesIdentity>
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+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="FOS" id="s_id_sa11824" metaid="s_id_sa11824" initialAmount="0.0" charge="0" compartment="s_id_ca182"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>RNA</celldesigner:class>
+<celldesigner:rnaReference>r_s_id_sa11824</celldesigner:rnaReference>
+<celldesigner:name>FOS</celldesigner:name>
+</celldesigner:speciesIdentity>
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+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PIP2" id="s_id_sa11759" metaid="s_id_sa11759" initialAmount="0.0" compartment="s_id_ca188"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Name: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate
+Synonyms: 1, 2-Diacyl-sn-glycero-3-phospho-(1'-myo-inositol-4', 5'-bisphosphate), 1-Phosphatidyl-1D-myo-inositol 4, 5-bisphosphate, 1-Phosphatidyl-1D-myo-inositol 4, 5-bisphosphate, 1-Phosphatidyl-D-myo-inositol 4, 5-bisphosphate, 1-Phosphatidyl-D-myo-inositol 4, 5-bisphosphate, Phosphatidyl-myo-inositol 4, 5-bisphosphate, Phosphatidyl-myo-inositol 4, 5-bisphosphate, Phosphatidylinositol-4, 5-bisphosphate, Phosphatidylinositol-4, 5-bisphosphate, PIP2, PIPP, PtsIns(4, 5)P2, PtsIns-4, 5-P2
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>innerSurface</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>PIP2</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A18348"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PKA_space_catalytic_space_subunit" id="s_id_csa1892" metaid="s_id_csa1892" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>PKA_space_catalytic_space_subunit</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ec-code:2.7.11.11"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="CNR1" id="s_id_sa11793" metaid="s_id_sa11793" initialAmount="0.0" compartment="s_id_ca188"><annotation><celldesigner:extension><celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11793</celldesigner:proteinReference>
+<celldesigner:name>CNR1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="GNAQ" id="s_id_sa11767" metaid="s_id_sa11767" initialAmount="0.0" charge="0" compartment="s_id_ca188"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11767</celldesigner:proteinReference>
+<celldesigner:name>GNAQ</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:interpro:IPR000654"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="ATP" id="s_id_sa11839" metaid="s_id_sa11839" initialAmount="0.0" charge="0" compartment="s_id_ca169"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Name: ATP
+Synonyms: Adenosine 5'-triphosphate, Adenosine triphosphate, ADENOSINE-5'-TRIPHOSPHATE, Adephos, Adetol, Adynol, Atipi, ATP, Atriphos, Cardenosine, Fosfobion, Glucobasin, H4atp, Myotriphos, Triadenyl, Triphosphaden, Recon metabolite: atp
+SemanticZoomLevelVisibility: 6
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+VMH database: <a href="http://vmh.uni.lu/#metabolite/atp">atp</a></body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>ATP</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A15422"/>
+</rdf:Bag>
+</bqbiol:is>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="PDEs" id="s_id_sa11845" metaid="s_id_sa11845" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11845</celldesigner:proteinReference>
+<celldesigner:name>PDEs</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:interpro:IPR023088"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="cofilin" id="s_id_csa1894" metaid="s_id_csa1894" initialAmount="0.0" charge="0" compartment="s_id_ca169"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>cofilin</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="TF_space_ELK1" id="s_id_csa1930" metaid="s_id_csa1930" initialAmount="0.0" charge="0" compartment="s_id_ca182"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>TF_space_ELK1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="HTR4" id="s_id_sa11789" metaid="s_id_sa11789" initialAmount="0.0" charge="0" compartment="s_id_ca188"><annotation><celldesigner:extension><celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11789</celldesigner:proteinReference>
+<celldesigner:name>HTR4</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="GNAL" id="s_id_sa11741" metaid="s_id_sa11741" initialAmount="0.0" charge="0" compartment="s_id_ca169"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: GNAL
+Name: G protein subunit alpha L
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11741</celldesigner:proteinReference>
+<celldesigner:name>GNAL</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:interpro:IPR000367"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="dendrite_space_extension" id="s_id_sa11699" metaid="s_id_sa11699" initialAmount="0.0" charge="0" compartment="s_id_ca168"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Name: dendrite extension
+SemanticZoomLevelVisibility: 6
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+Long distance growth of a single dendrite involved in cellular development.</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PHENOTYPE</celldesigner:class>
+<celldesigner:name>dendrite_space_extension</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0097484"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="CaMKII" id="s_id_csa1919" metaid="s_id_csa1919" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>CaMKII</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0005954"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="OPRM1" id="s_id_sa11792" metaid="s_id_sa11792" initialAmount="0.0" charge="0" compartment="s_id_ca188"><annotation><celldesigner:extension><celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11792</celldesigner:proteinReference>
+<celldesigner:name>OPRM1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="L_minus_type_space_calcium_space_channel_BR_Cav1.3_space_and_space_Cav1.2" id="s_id_csa1923" metaid="s_id_csa1923" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>outerSurface</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>L_minus_type_space_calcium_space_channel_BR_Cav1.3_space_and_space_Cav1.2</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:interpro:IPR005446"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="GNAS" id="s_id_sa11763" metaid="s_id_sa11763" initialAmount="0.0" charge="0" compartment="s_id_ca169"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: GNAS
+Name: GNAS complex locus
+Previous Symbols: GNAS1
+Synonyms: GNASXL, GPSA, NESP, NESP55, SCG6, SgVI
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11763</celldesigner:proteinReference>
+<celldesigner:name>GNAS</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:interpro:IPR000367"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="Calcineurin" id="s_id_csa1940" metaid="s_id_csa1940" initialAmount="0.0" charge="0" compartment="s_id_ca188"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>Calcineurin</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0004723"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:mesh:D019703"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="EEF2K" id="s_id_sa11748" metaid="s_id_sa11748" initialAmount="0.0" charge="0" compartment="s_id_ca173"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: EEF2K
+Name: eukaryotic elongation factor 2 kinase
+Synonyms: eEF-2K
+HGNC_ID: 24615
+EntrezGene_ID: 29904
+RefSeq_ID: NM_013302
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11748</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+<celldesigner:modification residue="rs1" state="phosphorylated"> </celldesigner:modification>
+<celldesigner:modification residue="rs2" state="ubiquitinated"> </celldesigner:modification>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>EEF2K</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:24615"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_013302"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:EEF2K"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:O00418"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000103319"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:29904"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="CDK5" id="s_id_sa11774" metaid="s_id_sa11774" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11774</celldesigner:proteinReference>
+<celldesigner:name>CDK5</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="s3264" id="s_id_sa11758" metaid="s_id_sa11758" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>DEGRADED</celldesigner:class>
+<celldesigner:name>s3264</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="MAP2" id="s_id_sa11695" metaid="s_id_sa11695" initialAmount="0.0" charge="0" compartment="s_id_ca168"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: MAP2
+Name: microtubule associated protein 2
+Synonyms: MAP2A, MAP2B, MAP2C
+HGNC_ID: 6839
+EntrezGene_ID: 4133
+RefSeq_ID: NM_001039538
+SemanticZoomLevelVisibility: 6
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11695</celldesigner:proteinReference>
+<celldesigner:name>MAP2</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_001039538"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:P11137"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000078018"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:MAP2"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:4133"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:6839"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="NMDA_space_receptor" id="s_id_csa1905" metaid="s_id_csa1905" initialAmount="0.0" charge="0" compartment="s_id_ca188"><annotation><celldesigner:extension><celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>NMDA_space_receptor</celldesigner:name>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0017146"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="calpain_minus_1" id="s_id_csa1912" metaid="s_id_csa1912" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>calpain_minus_1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:interpro:IPR029643"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="MAPK_space_pathway" id="s_id_sa11785" metaid="s_id_sa11785" initialAmount="0.0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PHENOTYPE</celldesigner:class>
+<celldesigner:name>MAPK_space_pathway</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isEncodedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0000165"/>
+</rdf:Bag>
+</bqbiol:isEncodedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="DUSP1" id="s_id_sa11825" metaid="s_id_sa11825" initialAmount="0.0" charge="0" compartment="s_id_ca182"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>RNA</celldesigner:class>
+<celldesigner:rnaReference>r_s_id_sa11825</celldesigner:rnaReference>
+<celldesigner:name>DUSP1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="CaMKII" id="s_id_csa1936" metaid="s_id_csa1936" initialAmount="0.0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:state>
+<celldesigner:listOfStructuralStates>
+<celldesigner:structuralState structuralState="phosphorylated">phosphorylated</celldesigner:structuralState></celldesigner:listOfStructuralStates>
+</celldesigner:state>
+<celldesigner:name>CaMKII</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="RASGRP2" id="s_id_sa11787" metaid="s_id_sa11787" initialAmount="0.0" charge="0" compartment="s_id_ca173"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: RASGRP2
+Name: RAS guanyl releasing protein 2
+Synonyms: CALDAG-GEFI
+HGNC_ID: 9879
+EntrezGene_ID: 10235
+RefSeq_ID: NM_153819
+SemanticZoomLevelVisibility: 4
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11787</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>RASGRP2</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_153819"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:RASGRP2"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:9879"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:Q7LDG7"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000068831"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:10235"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="LRRK2" id="s_id_sa11710" metaid="s_id_sa11710" initialAmount="0.0" charge="0" compartment="s_id_ca168"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: LRRK2
+Name: leucine rich repeat kinase 2
+Previous Symbols: PARK8
+Synonyms: DKFZp434H2111, FLJ45829, RIPK7, ROCO2
+HGNC_ID: 18618
+EntrezGene_ID: 120892
+RefSeq_ID: XM_058513
+SemanticZoomLevelVisibility: 6
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11710</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfStructuralStates>
+<celldesigner:structuralState structuralState="mutated R1441C">mutated R1441C</celldesigner:structuralState></celldesigner:listOfStructuralStates>
+<celldesigner:listOfModifications>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>LRRK2</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:120892"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:Q5S007"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:18618"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:XM_058513"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000188906"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:LRRK2"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="ITPR3" id="s_id_sa11716" metaid="s_id_sa11716" initialAmount="0.0" charge="0" compartment="s_id_ca187"><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Symbol: ITPR3
+Name: inositol 1,4,5-trisphosphate receptor type 3
+Synonyms: IP3R3
+HGNC_ID: 6182
+EntrezGene_ID: 3710
+RefSeq_ID: NM_002224
+SemanticZoomLevelVisibility: 7
+TransparencyZoomLevelVisibility: 0
+Charge: 0
+
+</body></html></notes>
+<annotation><celldesigner:extension><celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa11716</celldesigner:proteinReference>
+<celldesigner:name>ITPR3</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NM_002224"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc.symbol:ITPR3"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:Q14573"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:6182"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:3710"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ensembl:ENSG00000096433"/>
+</rdf:Bag>
+</bqbiol:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="s391" id="s_id_sa11775" metaid="s_id_sa11775" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>DEGRADED</celldesigner:class>
+<celldesigner:name>s391</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="serotonin" id="s_id_sa11791" metaid="s_id_sa11791" initialAmount="0.0" compartment="default"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>serotonin</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species name="LRRK2:PKAR2B:PKAC" id="s_id_csa1888" metaid="s_id_csa1888" initialAmount="0.0" charge="0" compartment="s_id_ca173"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>LRRK2:PKAR2B:PKAC</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+</listOfSpecies>
+<listOfReactions>
+<reaction metaid="re5811" id="re5811" name="" reversible="false" >
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType><celldesigner:baseReactants>
+<celldesigner:baseReactant species="s_id_sa11737" alias="sa11737" >
+<celldesigner:linkAnchor position="N"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s_id_sa11758" alias="sa11758" >
+<celldesigner:linkAnchor position="S"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0" >
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
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+</listOfProducts>
+</reaction>
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+<annotation>
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+<celldesigner:linkAnchor position="N"/>
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+<celldesigner:baseProducts>
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+<celldesigner:linkAnchor position="SSW"/>
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+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0" >
+<celldesigner:listOfLineDirection>
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+<celldesigner:line width="1.0" color="FF000000" type="Straight" />
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+<bqbiol:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pubmed:17408758"/>
+</rdf:Bag>
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+</rdf:RDF>
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+<listOfReactants>
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+<listOfProducts>
+<speciesReference species="s_id_csa1923" >
+<annotation>
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+</listOfProducts>
+</reaction>
+</listOfReactions>
+<notes>For information on content, functionalities and referencing the Parkinson's disease map, click <a href="http://pdmap.uni.lu" target="_blank">here</a> .</notes></model></sbml>
\ No newline at end of file