bio added

cyto_proposal_draft.html

@@ -22,16 +22,16 @@ w\:* {behavior:url(#default#VML);}
  <o:DocumentProperties>
   <o:Author>Abhas Bhattacharya</o:Author>
   <o:LastAuthor>Abhas Bhattacharya</o:LastAuthor>
-  <o:Revision>2</o:Revision>
+  <o:Revision>7</o:Revision>
-  <o:TotalTime>11</o:TotalTime>
+  <o:TotalTime>44</o:TotalTime>
   <o:Created>2013-04-23T21:30:00Z</o:Created>
-  <o:LastSaved>2013-04-23T21:30:00Z</o:LastSaved>
+  <o:LastSaved>2013-04-30T21:31:00Z</o:LastSaved>
   <o:Pages>5</o:Pages>
-  <o:Words>1725</o:Words>
+  <o:Words>1901</o:Words>
-  <o:Characters>9836</o:Characters>
+  <o:Characters>10836</o:Characters>
-  <o:Lines>81</o:Lines>
+  <o:Lines>90</o:Lines>
-  <o:Paragraphs>23</o:Paragraphs>
+  <o:Paragraphs>25</o:Paragraphs>
-  <o:CharactersWithSpaces>11538</o:CharactersWithSpaces>
+  <o:CharactersWithSpaces>12712</o:CharactersWithSpaces>
   <o:Version>14.00</o:Version>
  </o:DocumentProperties>
  <o:OfficeDocumentSettings>
@@ -43,8 +43,6 @@ w\:* {behavior:url(#default#VML);}
 href="cyto_proposal_draft_files/colorschememapping.xml">
 <!--[if gte mso 9]><xml>
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-  <w:SpellingState>Clean</w:SpellingState>
-  <w:GrammarState>Clean</w:GrammarState>
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   <w:PunctuationKerning/>
@@ -67,6 +65,7 @@ href="cyto_proposal_draft_files/colorschememapping.xml">
    <w:DontFlipMirrorIndents/>
    <w:OverrideTableStyleHps/>
   </w:Compatibility>
+  <w:BrowserLevel>MicrosoftInternetExplorer4</w:BrowserLevel>
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    <m:mathFont m:val="Cambria Math"/>
    <m:brkBin m:val="before"/>
@@ -373,9 +372,8 @@ href="cyto_proposal_draft_files/colorschememapping.xml">
 	panose-1:2 11 6 4 3 5 4 4 2 4;
 	mso-font-charset:0;
 	mso-generic-font-family:swiss;
-	mso-font-format:other;
 	mso-font-pitch:variable;
-	mso-font-signature:3 0 0 0 1 0;}
+	mso-font-signature:-520081665 -1073717157 41 0 66047 0;}
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@@ -576,8 +574,7 @@ p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
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 	font-family:"Tahoma","sans-serif";
 	mso-fareast-font-family:Calibri;
-	mso-fareast-theme-font:minor-latin;
+	mso-fareast-theme-font:minor-latin;}
-	mso-bidi-font-family:Tahoma;}
 p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
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@@ -749,12 +746,6 @@ span.BalloonTextChar
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 	mso-bidi-font-family:Tahoma;}
-span.SpellE
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-	mso-spl-e:yes;}
-span.GramE
-	{mso-style-name:"";
-	mso-gram-e:yes;}
 .MsoChpDefault
 	{mso-style-type:export-only;
 	mso-default-props:yes;
@@ -1159,38 +1150,6 @@ div.WordSection1
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 ol
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 ul
@@ -1249,9 +1208,9 @@ mso-border-bottom-themecolor:accent1;padding:0in 0in 4.0pt 0in'>
 Cytoscape 3.0 file formats.</p>
 
 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>The idea is based
-upon suggested Idea 19: JavaScript JSON convertors for graph file formats, but
+upon suggested Idea 19: JavaScript JSON convertors for graph file formats, but I
-I would like to drop the word “graph” from it, because this project will
+would like to drop the word “graph” from it, because this project will support
-support virtually all formats accepted by Cytoscape <span class=GramE>3.0 .</span></p>
+virtually all formats accepted by Cytoscape 3.0 .</p>
 
 <h1>Synopsis:</h1>
 
@@ -1274,14 +1233,13 @@ generation of json representation.</p>
 
 <p class=MsoNormal>The Cytoscape 3.0 file formats that will be supported are:</p>
 
-<p class=MsoNormal>Xgmml, Graphml, Sif, Nnf, Gml (<span class=GramE>,Csv</span>,
+<p class=MsoNormal>Xgmml, Graphml, Sif, Nnf, Gml (,Csv, Xlsx).</p>
-Xlsx).</p>
 
 <p class=MsoNormal>They are arranged according to their priority and so this is
 the order in which their json converters will be implemented. The last two (in
 bracket) will be kept as extras, meaning that they will be implemented only if
-the project is finished well before the deadline (see the timeline for details<span
+the project is finished well before the deadline (see the timeline for details)
-class=GramE>) .</span></p>
+.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
  id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
@@ -1304,12 +1262,12 @@ class=GramE>) .</span></p>
  <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
  <o:lock v:ext="edit" aspectratio="t"/>
 </v:shapetype><v:shape id="Picture_x0020_2" o:spid="_x0000_i1026" type="#_x0000_t75"
- alt="Description: Description: C:\Users\Abhas_2\Desktop\cyto\cyto_proposal.png"
+ alt="Description: Description: Description: C:\Users\Abhas_2\Desktop\cyto\cyto_proposal.png"
  style='width:468pt;height:312pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="cyto_proposal_draft_files/image001.png" o:title="cyto_proposal"/>
 </v:shape><![endif]--><![if !vml]><img width=624 height=416
-src="cyto_proposal_draft_files/image002.png"
+src="cyto_proposal_draft_files/image001.png"
-alt="Description: Description: C:\Users\Abhas_2\Desktop\cyto\cyto_proposal.png"
+alt="Description: Description: Description: C:\Users\Abhas_2\Desktop\cyto\cyto_proposal.png"
 v:shapes="Picture_x0020_2"><![endif]></span></p>
 
 <p class=MsoNormal>Now, this is how I plan to deal with each of them.</p>
@@ -1318,13 +1276,12 @@ v:shapes="Picture_x0020_2"><![endif]></span></p>
 style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 </span></span></span><![endif]>Xgmml: This is the top priority format and hence
-will be dealt with first. Xml parsers available in native <span class=SpellE>javascript</span>
+will be dealt with first. Xml parsers available in native javascript and jquery
-and <span class=SpellE>jquery</span> will be used for parsing the xgmml file.
+will be used for parsing the xgmml file. Then some JavaScript code (using
-Then some JavaScript code (using looping and if needed, regular expressions)
+looping and if needed, regular expressions) will deal with the parsed xml file
-will deal with the parsed xml file to convert them correctly into <span
+to convert them correctly into javascript variables and objects. Finally, they
-class=SpellE>javascript</span> variables and objects. Finally, they can be used
+can be used to generate its json representation. (Maybe, take some inspiration
-to generate its json representation. (Maybe, take some inspiration from this
+from this library in Gremlin (written in java): <a
-library in Gremlin (written in java): <a
 href="https://github.com/tinkerpop/blueprints/wiki/GraphSON-Reader-and-Writer-Library">https://github.com/tinkerpop/blueprints/wiki/GraphSON-Reader-and-Writer-Library</a>
 )</p>
 
@@ -1362,9 +1319,8 @@ Symbol'><span style='mso-list:Ignore'>
 text-indent:-.25in;mso-list:l0 level2 lfo6'><![if !supportLists]><span
 style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span></span><![endif]>Whether it is a “node” or <span class=GramE>a</span>
+</span></span></span><![endif]>Whether it is a “node” or a “edge” is
-“edge” is represented by “group” in json. All its data is stored in the “data”
+represented by “group” in json. All its data is stored in the “data” object.</p>
-object.</p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
 auto;text-indent:-.25in;mso-list:l0 level2 lfo6'><![if !supportLists]><span
@@ -1433,18 +1389,19 @@ style='mso-spacerun:yes'>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
 style='mso-spacerun:yes'>    </span>&lt;graphics width=&quot;1&quot;
-fill=&quot;#<span class=SpellE>fcfffd</span>&quot;&gt;<o:p></o:p></span></p>
+fill=&quot;#fcfffd&quot;&gt;<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-spacerun:yes'>        </span>&lt;att name=&quot;<span class=SpellE>cytoscapeNodeGraphicsAttributes</span>&quot;&gt;<o:p></o:p></span></p>
+style='mso-spacerun:yes'>        </span>&lt;att
+name=&quot;cytoscapeNodeGraphicsAttributes&quot;&gt;<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-spacerun:yes'>            </span>&lt;att name=&quot;<span
+style='mso-spacerun:yes'>            </span>&lt;att
-class=SpellE>nodeTransparency</span>&quot; value=&quot;1.0&quot;/&gt;<o:p></o:p></span></p>
+name=&quot;nodeTransparency&quot; value=&quot;1.0&quot;/&gt;<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-spacerun:yes'>            </span>&lt;att name=&quot;<span
+style='mso-spacerun:yes'>            </span>&lt;att
-class=SpellE>nodeLabelFont</span>&quot; value=&quot;Default-0-12&quot;/&gt;<o:p></o:p></span></p>
+name=&quot;nodeLabelFont&quot; value=&quot;Default-0-12&quot;/&gt;<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
 style='mso-spacerun:yes'>        </span>&lt;/att&gt;<o:p></o:p></span></p>
@@ -1465,44 +1422,46 @@ style='font-size:14.0pt;line-height:115%;font-family:"Arial","sans-serif"'> )<o:
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'>[<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-spacerun:yes'>    </span><span class=GramE>{ “</span>data”: {<o:p></o:p></span></p>
+style='mso-spacerun:yes'>    </span>{ “data”: {<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-spacerun:yes'>                </span>&quot;<span class=GramE>id</span>&quot;:&quot;YKR026C&quot;,<o:p></o:p></span></p>
+style='mso-spacerun:yes'>               
+</span>&quot;id&quot;:&quot;YKR026C&quot;,<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-spacerun:yes'>                </span>&quot;<span class=GramE>label</span>&quot;:&quot;YBR043C&quot;,<o:p></o:p></span></p>
+style='mso-spacerun:yes'>               
+</span>&quot;label&quot;:&quot;YBR043C&quot;,<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
 style='mso-spacerun:yes'>                </span>&quot;gal1RGexp&quot;:0.454,<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
 style='mso-spacerun:yes'>                </span>&quot;GO Cellular
-Component&quot;<span class=GramE>:[</span>&quot;cell&quot;, &quot;cell
+Component&quot;:[&quot;cell&quot;, &quot;cell part&quot;],<o:p></o:p></span></p>
-part&quot;],<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-spacerun:yes'>                </span>&quot;<span class=GramE>graphics</span>&quot;:{&quot;width&quot;:&quot;1&quot;,<o:p></o:p></span></p>
+style='mso-spacerun:yes'>               
+</span>&quot;graphics&quot;:{&quot;width&quot;:&quot;1&quot;,<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-spacerun:yes'>                            </span>&quot;<span
+style='mso-spacerun:yes'>                           
-class=GramE>fill</span>&quot;:&quot;#<span class=SpellE>fcfffd</span>&quot;,<o:p></o:p></span></p>
+</span>&quot;fill&quot;:&quot;#fcfffd&quot;,<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-spacerun:yes'>                            </span>&quot;<span
+style='mso-spacerun:yes'>   </span><span
-class=SpellE><span class=GramE>cytoscapeNodeGraphicsAttributes</span></span>&quot;:{<o:p></o:p></span></p>
+style='mso-spacerun:yes'>                         </span>&quot;cytoscapeNodeGraphicsAttributes&quot;:{<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
 style='mso-spacerun:yes'>                                                               
-</span>&quot;<span class=GramE>nodeTransparency</span>&quot;:&quot;1.0&quot;,<o:p></o:p></span></p>
+</span>&quot;nodeTransparency&quot;:&quot;1.0&quot;,<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
 style='mso-spacerun:yes'>                                                               
-</span>&quot;<span class=GramE>nodeLabelFont</span>&quot;:&quot;Default-0-12&quot;<o:p></o:p></span></p>
+</span>&quot;nodeLabelFont&quot;:&quot;Default-0-12&quot;<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-spacerun:yes'>       </span><span
+style='mso-spacerun:yes'>          </span><span
-style='mso-spacerun:yes'>                                                       </span>}<o:p></o:p></span></p>
+style='mso-spacerun:yes'>                                                    </span>}<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
 style='mso-spacerun:yes'>                            </span>}<o:p></o:p></span></p>
@@ -1511,8 +1470,7 @@ style='mso-spacerun:yes'>
 style='mso-spacerun:yes'>            </span>},<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-spacerun:yes'>      </span>&quot;<span class=GramE>group</span>&quot;:
+style='mso-spacerun:yes'>      </span>&quot;group&quot;: &quot;nodes&quot;<o:p></o:p></span></p>
-&quot;nodes&quot;<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
 style='mso-spacerun:yes'>    </span>}<o:p></o:p></span></p>
@@ -1525,9 +1483,9 @@ style='mso-spacerun:yes'>
 style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 </span></span></span><![endif]>Graphml:<span style='mso-spacerun:yes'> 
-</span>Graphml is also <span class=GramE>a</span> xml-based format, so the
+</span>Graphml is also a xml-based format, so the implementation process is
-implementation process is same as that of the previous one. Only the code will
+same as that of the previous one. Only the code will be different to take care
-be different to take care of the syntax difference of these formats.</p>
+of the syntax difference of these formats.</p>
 
 <p class=MsoNormal style='margin-left:.5in'>Conversion guideline:</p>
 
@@ -1535,8 +1493,7 @@ be different to take care of the syntax difference of these formats.</p>
 text-indent:-.25in;mso-list:l0 level2 lfo6'><![if !supportLists]><span
 style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span></span><![endif]>Make use of the graphml – attribute values <span
+</span></span></span><![endif]>Make use of the graphml – attribute values ( <a
-class=GramE>( </span><a
 href="http://graphml.graphdrawing.org/primer/graphml-primer.html#AttributesValues">http://graphml.graphdrawing.org/primer/graphml-primer.html#AttributesValues</a>
 ) to know the attribute type and the default values, if present.</p>
 
@@ -1546,14 +1503,13 @@ style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 </span></span></span><![endif]>All the<span style='mso-spacerun:yes'> 
 </span>“key” attributes in the &lt;data&gt; tags will be converted into json
-data of type “<span class=SpellE>attr.type</span>” (which are provided as
+data of type “attr.type” (which are provided as graphml – attribute values )</p>
-graphml – attribute values )</p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
 auto;text-indent:-.25in;mso-list:l0 level2 lfo6'><![if !supportLists]><span
 style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span></span><![endif]>Convert complex types <span class=GramE>( </span><a
+</span></span></span><![endif]>Convert complex types ( <a
 href="http://graphml.graphdrawing.org/primer/graphml-primer.html#Complex">http://graphml.graphdrawing.org/primer/graphml-primer.html#Complex</a>
 ) into objects.</p>
 
@@ -1569,7 +1525,7 @@ do-able.)</p>
 <p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
 
 <p class=MsoListParagraphCxSpMiddle>[Side-by-side examples are not provided for
-this one, as they are pretty easy to understand<span class=GramE>. ]</span></p>
+this one, as they are pretty easy to understand. ]</p>
 
 <p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
 
@@ -1579,12 +1535,12 @@ this one, as they are pretty easy to understand<span class=GramE>. ]</span></p>
 a small chart for reference:</p>
 
 <p class=MsoListParagraphCxSpLast><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_3" o:spid="_x0000_i1025" type="#_x0000_t75" alt="Description: Description: C:\Users\Abhas_2\Desktop\cyto\cyto_implementation.png"
+ id="Picture_x0020_3" o:spid="_x0000_i1025" type="#_x0000_t75" alt="Description: Description: Description: C:\Users\Abhas_2\Desktop\cyto\cyto_implementation.png"
  style='width:591.75pt;height:345pt;visibility:visible;mso-wrap-style:square'>
- <v:imagedata src="cyto_proposal_draft_files/image003.png" o:title="cyto_implementation"/>
+ <v:imagedata src="cyto_proposal_draft_files/image002.png" o:title="cyto_implementation"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=789 height=460
-src="cyto_proposal_draft_files/image003.png"
+src="cyto_proposal_draft_files/image002.png"
-alt="Description: Description: C:\Users\Abhas_2\Desktop\cyto\cyto_implementation.png"
+alt="Description: Description: Description: C:\Users\Abhas_2\Desktop\cyto\cyto_implementation.png"
 v:shapes="Picture_x0020_3"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1592,8 +1548,8 @@ v:shapes="Picture_x0020_3"><![endif]></span></p>
 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo6'><![if !supportLists]><span
 style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span></span><![endif]>Sif and Nnf: Very simple jS code needs to be
+</span></span></span><![endif]>Sif and Nnf: Very simple jS code needs to be written
-written to take care of these file formats. There is already a python-based
+to take care of these file formats. There is already a python-based
 implementation of these converters (written by me) available at <a
 href="https://github.com/bendtherules/GSOC_13/tree/master/nnf_and_sif_to_json_py%20%20">https://github.com/bendtherules/GSOC_13/tree/master/nnf_and_sif_to_json_py
 </a><span style='mso-spacerun:yes'> </span>. <span style='background:lightgrey;
@@ -1606,10 +1562,9 @@ in Nnf will be taken care of (stored in the
 style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
 style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 </span></span></span><![endif]>GML:<span style='mso-spacerun:yes'>  </span>A
-custom-made parser needs to be built based on regular expressions (native <span
+custom-made parser needs to be built based on regular expressions (native js or
-class=SpellE>js</span> or possibly using xregexp library <a
+possibly using xregexp library <a href="http://xregexp.com/">http://xregexp.com/</a>
-href="http://xregexp.com/">http://xregexp.com/</a> ). The rest of the plan is
+). The rest of the plan is the same as that of xgmml, only this new parser will
-the same as that of <span class=GramE>xgmml,</span> only this new parser will
 be used.<span style='mso-spacerun:yes'>  </span>As XGMML is the successor of
 GML, the conversion guidelines used in xgmml should suffice (only the idea of
 tags are not present here, everything is separated by space/tab).</p>
@@ -1618,40 +1573,37 @@ tags are not present here, everything is separated by space/tab).</p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-size:14.0pt;
 line-height:115%;background:aqua;mso-highlight:aqua'>GML</span><span
-style='font-size:14.0pt;line-height:115%'> <span class=GramE>( </span><a
+style='font-size:14.0pt;line-height:115%'> ( <a
 href="https://github.com/bendtherules/GSOC_13/blob/master/Proposal/preview.gml">https://github.com/bendtherules/GSOC_13/blob/master/Proposal/preview.gml</a>
 )<o:p></o:p></span></p>
 
-<p class=MsoNormal style='margin-left:.5in'><span class=GramE><span
+<p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'>node<o:p></o:p></span></p>
-style='font-family:"Arial","sans-serif"'>node</span></span><span
-style='font-family:"Arial","sans-serif"'><o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'>[<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-tab-count:1'>            </span><span class=GramE>id</span><span
+style='mso-tab-count:1'>            </span>id<span style='mso-tab-count:1'>         </span>0<o:p></o:p></span></p>
-style='mso-tab-count:1'>         </span>0<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-tab-count:1'>            </span><span class=GramE>label</span><span
+style='mso-tab-count:1'>            </span>label<span style='mso-tab-count:
-style='mso-tab-count:1'>     </span>&quot;YKR026C&quot;<o:p></o:p></span></p>
+1'>     </span>&quot;YKR026C&quot;<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-tab-count:1'>            </span><span class=GramE>graphics</span><o:p></o:p></span></p>
+style='mso-tab-count:1'>            </span>graphics<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
 style='mso-tab-count:1'>            </span>[<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-tab-count:2'>                        </span><span class=GramE>x</span><span
+style='mso-tab-count:2'>                        </span>x<span style='mso-tab-count:
-style='mso-tab-count:1'>          </span>1916.0<o:p></o:p></span></p>
+1'>          </span>1916.0<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-tab-count:2'>                        </span><span class=GramE>type</span><span
+style='mso-tab-count:2'>                        </span>type<span
 style='mso-tab-count:1'>     </span>&quot;ellipse&quot;<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-tab-count:2'>                        </span><span class=GramE>fill</span><span
+style='mso-tab-count:2'>                        </span>fill<span
 style='mso-tab-count:1'>         </span>&quot;#E1E1E1&quot;<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
@@ -1671,24 +1623,25 @@ style='font-size:14.0pt;line-height:115%;mso-bidi-font-family:Arial'> )<o:p></o:
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'>[<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-spacerun:yes'>    </span><span class=GramE>{ data</span>: {<o:p></o:p></span></p>
+style='mso-spacerun:yes'>    </span>{ data: {<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-spacerun:yes'>                </span>&quot;<span class=GramE>id</span>&quot;:0,<o:p></o:p></span></p>
+style='mso-spacerun:yes'>                </span>&quot;id&quot;:0,<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-spacerun:yes'>                </span>&quot;<span class=GramE>label</span>&quot;:&quot;YKR026C&quot;,<o:p></o:p></span></p>
+style='mso-spacerun:yes'>               
+</span>&quot;label&quot;:&quot;YKR026C&quot;,<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-spacerun:yes'>                </span>&quot;<span class=GramE>graphics</span>&quot;:{&quot;x&quot;:1916.0,<o:p></o:p></span></p>
+style='mso-spacerun:yes'>               
+</span>&quot;graphics&quot;:{&quot;x&quot;:1916.0,<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-spacerun:yes'>                            </span>&quot;<span
+style='mso-spacerun:yes'>                            </span>&quot;type&quot;:&quot;ellipse&quot;,<o:p></o:p></span></p>
-class=SpellE><span class=GramE>type</span>&quot;:&quot;ellipse</span>&quot;,<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-spacerun:yes'>                            </span>&quot;<span
+style='mso-spacerun:yes'>                           
-class=GramE>fill</span>&quot;:&quot;#E1E1E1&quot;,<o:p></o:p></span></p>
+</span>&quot;fill&quot;:&quot;#E1E1E1&quot;,<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
 style='mso-spacerun:yes'>                            </span>}<o:p></o:p></span></p>
@@ -1697,8 +1650,7 @@ style='mso-spacerun:yes'>
 style='mso-spacerun:yes'>            </span>},<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
-style='mso-spacerun:yes'>      </span>&quot;<span class=GramE>group</span>&quot;:
+style='mso-spacerun:yes'>      </span>&quot;group&quot;: &quot;nodes&quot;<o:p></o:p></span></p>
-&quot;nodes&quot;<o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
 style='mso-spacerun:yes'>    </span>}<o:p></o:p></span></p>
@@ -1709,15 +1661,14 @@ style='mso-spacerun:yes'>
 
 <p class=MsoNormal>Few words on the extras:</p>
 
-<p class=MsoNormal>These extras will be done only if there is ample time left
+<p class=MsoNormal>These extras will be done only if there is ample time left after
-after the completion of the whole project, so there is no way that they will
+the completion of the whole project, so there is no way that they will harm the
-harm the main project. I am aware that new GSOC applicants like me tend to
+main project. I am aware that new GSOC applicants like me tend to propose a lot
-propose a lot more than they can actually complete, so I have tried not to fall
+more than they can actually complete, so I have tried not to fall in that trap.
-in that trap. But these extras are here, because I plan to do them in the
+But these extras are here, because I plan to do them in the future, within or
-future, within or after GSOC.<span style='mso-spacerun:yes'>  </span>Also, as a
+after GSOC.<span style='mso-spacerun:yes'>  </span>Also, as a side note, in
-side note, in future, I wish to release this codes as a separate jS library for
+future, I wish to release this codes as a separate jS library for converting
-converting customized-xml formats into json (I hope my mentoring org will allow
+customized-xml formats into json (I hope my mentoring org will allow this).</p>
-this).</p>
 
 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l0 level1 lfo6'><![if !supportLists]><span
 style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
@@ -1730,14 +1681,14 @@ style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
 style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 </span></span></span><![endif]>Xlsx: <span style='color:red;background:lightgrey;
 mso-highlight:lightgrey'>**Potential License Issue**</span><span
-style='color:red'> </span><span class=GramE>This</span> is the most challenging
+style='color:red'> </span>This is the most challenging part. I wouldn’t have
-part. I wouldn’t have tried this if there was no cross-browser external library
+tried this if there was no cross-browser external library to read and write
-to read and write xlsx format. But thankfully and quite surprisingly, there is
+xlsx format. But thankfully and quite surprisingly, there is one called Xlsx.js
-one called Xlsx.js <a href="https://github.com/stephen-hardy/xlsx.js">https://github.com/stephen-hardy/xlsx.js</a>
+<a href="https://github.com/stephen-hardy/xlsx.js">https://github.com/stephen-hardy/xlsx.js</a>
 . I am not much sure if I can pull off this part, but I am still including this
 in the proposal mostly for my inspiration than anything else. Also, I know that
 the Cytoscape project originally supported .xls, but I think its best kept to
-Microsoft Excel for converting .xls into .<span class=GramE>xlsx .</span></p>
+Microsoft Excel for converting .xls into .xlsx .</p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
@@ -1846,7 +1797,7 @@ mso-bidi-font-size:11.0pt;line-height:115%;mso-bidi-font-family:Calibri;
 mso-bidi-theme-font:minor-latin'><span style='mso-list:Ignore'>7.<span
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>July
 30: Take a day off from coding and analyze what went right and wrong in the
-first-term. (How about a blog post<span class=GramE>? :</span>D)</p>
+first-term. (How about a blog post? :D)</p>
 
 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo8;
 tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
@@ -1894,8 +1845,8 @@ style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></span><![
 4 – September 16 (13 days): Buffer time (If everything is working, work on the
 extras) </p>
 
-<p class=MsoNormal>(Feedback will be obtained for all the converters from the
+<p class=MsoNormal>(Feedback will be obtained for all the converters from the community
-community and they will be given more importance than the extras)</p>
+and they will be given more importance than the extras)</p>
 
 <h1>Possible hurdles:</h1>
 
@@ -1923,8 +1874,8 @@ mso-bidi-font-size:11.0pt;line-height:115%;mso-bidi-font-family:Calibri;
 mso-bidi-theme-font:minor-latin'><span style='mso-list:Ignore'>3.<span
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>The
 input graph formats might not be well-formed (if manually created). (Maybe, add
-<span class=GramE>a</span> xml-checker and discard non well-formed files. Such
+a xml-checker and discard non well-formed files. Such a checker might not be
-a checker might not be possible in case of non-xml based formats. )</p>
+possible in case of non-xml based formats. )</p>
 
 <h1>What can I bring to the team?</h1>
 
@@ -1950,12 +1901,58 @@ super-excited about it, can
 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 </span></span></span><![endif]>I wish to learn some more about the core
-Cytoscape project but as I am not a Java <span class=GramE>developer,</span> I
+Cytoscape project but as I am not a Java developer, I wish to linger with the
-wish to linger with the Cytoscape.js project.</p>
+Cytoscape.js project.</p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
-<h1>Bio &lt;To be added soon&gt;</h1>
+<h1>Bio:</h1>
+
+<p class=MsoNormal><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Name:</b> Abhas
+Bhattacharya</p>
+
+<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Email:</b> <span
+style='mso-spacerun:yes'> </span><a href="mailto:abhasbhattacharya2@gmail.com">abhasbhattacharya2@gmail.com</a></p>
+
+<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Education:</b> Passed
+High School, Ongoing B. Tech (1<sup>st</sup> year) in Aerospace engineering at
+BESU ( <a href="http://www.becs.ac.in">www.becs.ac.in</a> )</p>
+
+<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Programming Languages
+of choice:</b> Python, Javascript, C, C++, Java (little).</p>
+
+<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Prior experience with
+open source development:<o:p></o:p></b></p>
+
+<p class=MsoNormal>I have some experience in working with Git and playing
+around with forked projects, but didn’t really contribute in them.</p>
+
+<p class=MsoNormal>Mostly, I am into game development, with python , gamemaker
+and javascript.</p>
+
+<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>What do I want to
+learn this summer?<o:p></o:p></b></p>
+
+<p class=MsoNormal>It will be a great opportunity for me to contribute to a
+project like Cytoscape by developing these converters which should help end-users.
+Being mostly a hobby developer, I want to learn how to collaborate and code on
+real-life open-source projects.</p>
+
+<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Any prior exposure to
+biology or bioinformatics?<o:p></o:p></b></p>
+
+<p class=MsoNormal>Studied biology till the 10<sup>th</sup> grade.</p>
+
+<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Any interest in
+learning a bit of biology this summer?<o:p></o:p></b></p>
+
+<p class=MsoNormal>Sure. As I was asking around in the google groups, I would
+like to know more about the working of the core Cytoscape project and also a
+little biology, whenever required.</p>
+
+<p class=MsoNormal>** End **</p>
 
 </div>
 

cyto_proposal_draft_files/filelist.xml

@@ -4,6 +4,5 @@
  <o:File HRef="colorschememapping.xml"/>
  <o:File HRef="image001.png"/>
  <o:File HRef="image002.png"/>
- <o:File HRef="image003.png"/>
  <o:File HRef="filelist.xml"/>
 </xml>