adding final slide, general polishing

2019/2019-06-25_file-naming/slides/final-notes.md

+
+# Final notes
+
+* plan ahead
+
+* follow guidelines of your team
+
+* ensure proper dissemination of your naming policy
+
+* consistency overrules personal preference

2019/2019-06-25_file-naming/slides/human_readable.md

@@ -2,12 +2,15 @@
 ## Human readable
 name carries information about content
 * use English
-* balance length against clarity
+
+* balance name length against clarity
+
 * don't be too creative and stay professional
+<!--   "PEPA_d-pic.jpeg" - a fourth **pic**ture from your paper on **P**erformance **E**valuation **P**rocess **A**lgebra -->
 
-  "PEPA_d-pic.jpeg" - a fourth **pic**ture from your paper on **P**erformance **E**valuation **P**rocess **A**lgebra
 
 * **never** use suffixes (or prefixes) like **"final"**, **"old"**, **"new"**, **"current"**, **"obsolete"**, **"recent"**, **"latest"**, **"best"**...
+
 * leave out meaningless words, e.g. "the", "and", "a", "file", "data" ...
 
 
@@ -25,7 +28,7 @@ name carries information about content
 
 | Bad named                 | Better name                                           |
 | ------------------------- | ----------------------------------------------------- |
-| myabstract.txt            | John_White-Sensitivity_of_PLFA_analyses-abstract.txt  |
-| samples_project_start.csv | PA324-samples_2019-12-11.csv                          |
-| ms_cresp_final.doc        | John_White-Cell_respiration-manuscript-2019-12-11.doc |
-| fig_1.png                 | John_White-Cell_respiration-fig_1-2019-12-11.png      |
+| myabstract.txt            | John-White_Sensitivity-of-PLFA-analyses_abstract.txt  |
+| samples_project_start.csv | PA324_samples_2019-12-11.csv                          |
+| ms_cresp_final.doc        | John-White_Cell-respiration_manuscript_2019-12-11.doc |
+| fig_1.png                 | John-White_Cell-respiration_fig-1_2019-12-11.png      |

2019/2019-06-25_file-naming/slides/list.json

@@ -4,11 +4,6 @@
         "attr": {
         }
     },
-    {
-        "filename": "overview.md",
-        "attr": {
-        }
-    },
     {
         "filename": "three_principles.md",
         "attr": {
@@ -30,7 +25,7 @@
         }
     },
     {
-        "filename": "take_away.md",
+        "filename": "final-notes.md",
         "attr": {
         }
     },

2019/2019-06-25_file-naming/slides/machine_readable.md

@@ -3,15 +3,15 @@
 
 * case sensitivity
 
-* special characters:
+* <span style="color:red">special characters</span>:
  **&#35;&#36;&#37;&#38;&#39;&#40;&#34;&#41;&#42;&#43;&#44; &#45;&#46;&#47;&#58;&#59;&#60;&#61;&#62;&#63;&#64;&#91;&#92; &#93;&#94;&#95;&#96;&#123;&#124;&#125;&#126;** and
 white characters like **space** or **tabulator**
 
-* accented characters:
+* <span style="color:red">accented characters</span>:
   **&#231;**, **&#228;**, **&#244;**,
  **&#283;**, **&#341;**, ...
 
-* lack of consistency:
+* <span style="color:red">lack of consistency</span>:
 ```
 2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFractions_B03.csv
 2013-06-26_BRAFWTNEGASSAY_Plasmid-Celline-100-1MutantFraction_B03.csv
@@ -29,22 +29,22 @@ So what should I use?
 * underscore "**&#95;**" to separate
 
 Example:  
-```
-projectID_method-name_sampleID_YYYY-MM-DD.ext
-Author-Name_Paper-Name_manuscript_YYYY-MM-DD.doc
-```
+
+"projectID_method-name_sampleID_YYYY-MM-DD.ext"  
+"Author-Name_Paper-Name_manuscript_YYYY-MM-DD.doc"
+
 
 
 
 # Machine readable
-Real **ugly** names:
+**Ugly** names:
 ```
  "Hlad.jez.M-L-průtoky JíObj.z Ohře-od 10-2011.xlsx"
  "Finacial detailes BIocore 19/11/12.xls"
  "ATACseq1Londonmapped.bam"
 ```
 
-Nice names:
+**Nice** names:
 ```
 Hipo-1631_CA1_iba-1488_GFAP-647.tiff
 2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_A01.csv

2019/2019-06-25_file-naming/slides/mySlide.md

-## mySlide
-
-0. Subject 1
-1. Subject 2

2019/2019-06-25_file-naming/slides/ordering.md

@@ -2,9 +2,11 @@
 ## Default ordering
 use of inbuilt ordering
 
-*  terms in general-to-specific order - logical ordering
+*  terms in general-to-specific order - logical ordering  
+"projectID_method-name_sampleID_YYYY-MM-DD.ext"
 <!-- TODO -->
 * date first - chronological ordering
+
 * digits first - explicit ordering
 
 
@@ -13,8 +15,10 @@ use of inbuilt ordering
 use of inbuilt ordering
 
 * terms in general-to-specific order - logical ordering
+
 <!-- TODO -->
 * date first - chronological ordering
+
   ```
   2013-06-26_Plasmid_A01.csv
   2014-06-26_Plasmid_C02.csv  
@@ -31,8 +35,10 @@ use of inbuilt ordering
 use of inbuilt ordering
 
 * terms in general-to-specific order - logical ordering
+
 <!-- TODO -->
 * date first - chronological ordering
+
 * digits first - explicit ordering
   ```
   01_Plasmid_A01_2013-06-26.csv

2019/2019-06-25_file-naming/slides/overview.md

-## Overview
-
-0. Subject 1
-1. Subject 2
\ No newline at end of file

2019/2019-06-25_file-naming/slides/summary.md

+## Three main principles
+* Machine readable:
+   * easily search for files later
+   * easily narrow file lists based on names
+   * easily extract info from file names, e.g. by splitting, regex,...
+* Human readable:
+   * easily understand what the file is and what it contains
+   * easily share files with others
+* Plays well with default ordering:
+   * logically ordered/clustered
+   * fast manual search

2019/2019-06-25_file-naming/slides/take_away.md

-
-# TAKEAWAY

2019/2019-06-25_file-naming/slides/three_principles.md

@@ -5,9 +5,11 @@
    * easily search for files later
    * easily narrow file lists based on names
    * easily extract info from file names, e.g. by splitting, regex,...
+
 * Human readable:
    * easily understand what the file is and what it contains
    * easily share files with others
+   
 * Plays well with default ordering:
    * logically ordered/clustered
    * fast manual search