- Small improvement: reaction type list simplified in the export network (#1246)
- Small improvement: export to image allows to define size of the image (#955)
- Small improvement: progress bar on project upload changed into more verbose statements (#921)
- Small improvement: AVOGADRO unit type from SBML is parsed properly (#1612)
- Small improvement: data overlays have automatically generated legend (#205, #1061)
- Small improvement: list of users contains information about logged in users (#219)
- Small improvement: possibility to provide image coords as json file (#1307)
- Small improvement: possibility to show reaction name (#1355)
- Small improvement: export to SBML provides information about parent-child complex relation using multi package (#1478)
- Small improvement: converter name is case insensitive (#1615)
- Small improvement: modification residues can use different color then species if format allows (SBGN, SBML) (#1141)
- Small improvement: possibility to show element id (#1229)
- Small improvement: There is possibility to provide custom CSS style (#1017)
- Small improvement: API provides information about modifier type (#1085)
- Small improvement: map file for JavaScript is properly referenced (#1545)
- Small improvement: z-index for modification residues and structural states is imported from SBML file if available
- Small improvement: debian installation creates db.properties file that is readable only by tomcat user
- Small improvement: import/export of text objects in SBML supported (#1353)
- Small improvement: CellDesigner texts inside LayerText with name "text" are visible on the map and not transformed into pathways (#1335)
- Small improvement: when free space on device drops under 10MB images will not be generated to prevent using all space on HDD (#1389)
- Small improvement: additional validation to REST input added (#689)
- Small improvement: validation for projectId added when creating project using API
- Small improvement: additional SBGN-ML glyphs are supported: "biological activity", "outcome", "entity", "observable", "interaction" (#1624)
- Small improvement: additional SBGN-ML are supported: "interaction", "positive influence", "negative influence", "unknown influence", "absolute stimulation", "absolute inhibition" (#1624)
- Small improvement: additional annotations are supported: ExAC Gene, ExAC Transcript, ExAC Variant, LINCS Protein, LINCS Cell, GWAS Central Marker, GWAS Central Phentoype, GWAS Central Study, Cooperative Patent Classification, USPTO, Google Patents, MIRIAM Registry collection, ICD, PIRSF, Nucleotide Sequence Database, Wormpep, PROSITE, arXiv, ArrayExpress, SABIO-RK Reaction, Transport Classification Database, UniParc, MINT, Database of Interacting Proteins, Signaling Gateway, RESID, TAIR Protein, TAIR Gene, PeptideAtlas, GEO, Saccharomyces genome database pathways, MatrixDB, PubChem-bioassay, Pathway Commons, HOVERGEN, MACiE, Sequence Ontology, SABIO-RK Kinetic Record, Ligand-Gated Ion Channel database, Anatomical Therapeutic Chemical, PharmGKB Disease, PharmGKB Drug, TTD Target, NeuronDB, NeuroMorpho, BioSystems, CTD Disease, CTD Gene, BioNumbers, T3DB, Small Molecule Pathway Database, PhosphoSite Protein, TEDDY, KiSAO, Molecular Interactions Ontology, Cell Type Ontology, Brenda Tissue Ontology, GlycomeDB, ProDom, SMART, Conserved Domain Database, Relation Ontology, Molecular Modeling Database, IMEx, iRefWeb, Microbial Protein Interaction Database, PhosphoSite Residue, NeuroLex, SABIO-RK EC Record, Ontology of Physics for Biology, JWS Online, ModelDB, SubtiWiki, ABS, Aceview Worm, Animal Diversity Web, Affymetrix Probeset, AFTOL, Registry, AntWeb, APD, AphidBase Transcript, ArachnoServer, Antibiotic Resistance Genes Database, ArrayExpress Platform, ASAP, AspGD Locus, AspGD Protein, ATCC, Anatomical Therapeutic Chemical Vetinary, Animal TFDB Family, AutDB, BacMap Biography, BacMap Map, BDGP EST, BDGP insertion DB, BeetleBase, Bgee family, Bgee gene, Bgee organ, Bgee stage, BioCarta Pathway, BioCatalogue, BioCyc, SBML RDF Vocabulary, BioPortal, BioProject, BioSample, BitterDB Compound, BitterDB Receptor, BOLD Taxonomy, Broad Fungal Genome Initiative, BugBase Expt, BugBase Protocol, BYKdb, CAPS-DB, CATH domain, CATH superfamily, Animal Genome Cattle QTL, Cell Cycle Ontology, Canadian Drug Product Database, Cell Image Library, Candida Genome Database, CGSC Strain, CharProt, ChemDB, Animal Genome Chicken QTL, CLDB, ClinVar Record, COMBINE specifications, Compulyeast, Conoserver, Coriell Cell Repositories, CORUM, CryptoDB, CSA, Cell Signaling Technology Pathways, Cell Signaling Technology Antibody, Cube db, DailyMed, DARC, DATF, DBD, dbEST, DBG2 Introns, dbProbe, Degradome Database, DEPOD, Dictybase EST, Dictybase Gene, DisProt, DOMMINO, DOOR, Database of Quantitative Cellular Signaling: Model, Database of Quantitative Cellular Signaling: Pathway, DPV, DragonDB Allele, DragonDB DNA, DragonDB Locus, DragonDB Protein, DRSC, EchoBASE, EcoliWiki, EDAM Ontology, Experimental Factor Ontology, European Genome-phenome Archive Dataset, European Genome-phenome Archive Study, eggNOG, ELM, ENA, Ensembl Bacteria, Ensembl Fungi, Ensembl Metazoa, Ensembl Protists, EPD, FooDB Compound, F-SNP, FuncBase Fly, FuncBase Human, FuncBase Mouse, FuncBase Yeast, FungiDB, GenPept, Genome Properties, GiardiaDB, GLIDA GPCR, GLIDA Ligand, GlycoEpitope, Golm Metabolome Database, Golm Metabolome Database Analyte, Golm Metabolome Database GC-MS spectra, Golm Metabolome Database Profile, Golm Metabolome Database Reference Substance, GOA, GOLD genome, GOLD metadata, GPCRDB, Gramene genes, Gramene protein, Gramene QTL, Gramene Taxonomy, GreenGenes, GRIN Plant Taxonomy, GRSDB, GXA Expt, GXA Gene, HAMAP, HCVDB, Homeodomain Research, HGMD, HGNC Family, H-InvDb Locus, H-InvDb Protein, H-InvDb Transcript, HOGENOM, HOMD Sequence Metainformation, HOMD Taxonomy, HomoloGene, HPA, Human Proteome Map Peptide, Human Proteome Map Protein, HPRD, HSSP, HUGE, ICEberg element, ICEberg family, IDEAL, Identifiers.org Terms, Integrated Microbial Genomes Gene, Integrated Microbial Genomes Taxon, IMGT LIGM, InChI, InChIKey, Sequence Read Archive, IntAct Molecule, IRD Segment Sequence, ISFinder, ISSN, IUPHAR family, IUPHAR receptor, JAX Mice, JCGGDB, Japan Collection of Microorganisms, Japan Chemical Substance Dictionary, JSTOR, KEGG Disease, KEGG Environ, KEGG Genome, KEGG Metagenome, KEGG Module, LigandBox, Locus Reference Genomic, Mouse Adult Gross Anatomy, MaizeGDB Locus, Mathematical Modelling Ontology, MassBank, MedlinePlus, MEROPS Family, MEROPS Inhibitor, MetaboLights, METLIN, MicrosporidiaDB, MimoDB, MIPModDB, mirEX, MIRIAM Registry resource, miRNEST, MMRRC, MGED Ontology, Molbase, MycoBank, MycoBrowser leprae, MycoBrowser marinum, MycoBrowser smegmatis, MycoBrowser tuberculosis, NAPP, NARCIS, NASC code, National Bibliography Number, NITE Biological Research Center Catalogue, NCIm, NCIt, National Drug Code, NEXTDB, nextProt, NIAEST, NONCODE v3, NONCODE v4 Gene, NONCODE v4 Transcript, NORINE, NucleaRDB, Odor Molecules DataBase, OMA Group, OMA Protein, OMIA, OPM, ORCID, Olfactory Receptor Database, OriDB Saccharomyces, OriDB Schizosaccharomyces, Orphanet, Orphanet Rare Disease Ontology, OrthoDB, Oryzabase Gene, Oryzabase Mutant, Oryzabase Stage, Oryzabase Strain, Oryza Tag Line, P3DB Protein, P3DB Site, PaleoDB, PANTHER Node, PANTHER Pathway, PANTHER Pathway Component, PASS2, PaxDb Organism, PaxDb Protein, Pazar Transcription Factor, Protein Data Bank Ligand, Peroxibase, PharmGKB Gene, Phenol-Explorer, PhosphoPoint Kinase, PhosphoPoint Phosphoprotein, PhylomeDB, Phytozome Locus, NCI Pathway Interaction Database: Pathway, Animal Genome Pig QTL, PINA, PiroplasmaDB, PlasmoDB, CutDB, SubstrateDB, Protein Model Database, PMP, Plant Ontology, Pocketome, PolBase, PomBase, Protein Ontology, PRIDE Project, ProGlycProt, ProtClustDB, ProteomicsDB Peptide, ProteomicsDB Protein, ProtoNet Cluster, ProtoNet ProteinCard, PSCDB, Pseudomonas Genome Database, Protein Affinity Reagents, Pathway Ontology, REBASE, RFAM, Rat Genome Database qTL, Rat Genome Database strain, Rice Genome Annotation Project, RNA Modification Database, Rouge, SCOP, ScerTF, Spectral Database for Organic Compounds, Sol Genomics Network, Animal Genome Sheep QTL, SIDER Drug, SIDER Side Effect, SitEx, SNOMED CT, SoyBase, STAP, SubtiList, SUPFAM, TarBase, Tetrahymena Genome Database, TIGRFAMS, Tissue List, Tree of Life, TOPDB, TopFind, ToxoDB, TreeBASE, TreeFam, TrichDB, TriTrypDB, UBERON, uBio NameBank, UM-BBD Compound, UM-BBD Enzyme, UM-BBD Pathway, UM-BBD Reaction, UM-BBD Biotransformation Rule, UNII, Unimod, UniSTS, Unite, VariO, Vbase2, VBRC, VFDB Gene, VFDB Genus, ViralZone, VIRsiRNA, WikiGenes, Worfdb, Yeast Intron Database v3, YRC PDR, ZINC, WormBase RNAi, BindingDB, BioGRID, MEROPS, PRINTS, Ligand Expo, ISBN, PRIDE, FMA, GABI, Genatlas, GeneCards, GeneFarm, GeneTree, Gene Wiki, Allergome, AmoebaDB, Antibody, Xenbase, YDPM, Yeast Intron Database v4.3, YeTFasCo, UniPathway Reaction, SwissLipids, SEED Compound, SEED Reactions, OMIT, enviPath, Human Phenotype Ontology, MetaNetX chemical, MetaNetX compartment, MetaNetX reaction (#1610)
- Bug fix: API endpoints were exposed without 'api' prefix
- Bug fix: anonymous user could upload file using API
- Bug fix: when passing JSON in patch/post methods contentType was not checked
- Bug fix: API does not allow to create plugin with wrong md5 hash (#1074)
- Bug fix: when exporting to CellDesigner make sure that layer id is numeric (#16)
- Bug fix: Pathway name was not drawn when there was element with the same name inside Pathway (#1613)
- Bug fix: help dialog is closed automatically after Add Project dialog is closed (#1099)
- Bug fix: root url must be valid url pointing to minerva instance (#1689)
- Bug fix: there were missing lines when exporting truncation/dissotiation reaction to GPML (#1676)
- Bug fix: some SBML files were recognized as CellDesigner files (#1677)
- Bug fix: reaction middle was not highlighted (#1637)
- Bug fix: when accessing data from cache in parallel, sometimes unexpected exception was thrown (#1638)
- Bug fix: transcription factor color is set to black in monochromatic background (#1643)
- Bug fix: modifier line end points are not modified when importing from SBGN (#1648)
- Improvement: possibility to register map in minerva-net (#1595)