mirror of
https://github.com/bendtherules/Pages.git
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minor changes
This commit is contained in:
+66
-55
@@ -22,16 +22,16 @@ w\:* {behavior:url(#default#VML);}
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<o:DocumentProperties>
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<o:Author>Abhas Bhattacharya</o:Author>
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<o:LastAuthor>Abhas Bhattacharya</o:LastAuthor>
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<o:Revision>2</o:Revision>
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<o:TotalTime>248</o:TotalTime>
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<o:Created>2013-04-22T16:28:00Z</o:Created>
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<o:LastSaved>2013-04-22T16:28:00Z</o:LastSaved>
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<o:Revision>4</o:Revision>
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<o:TotalTime>8</o:TotalTime>
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<o:Created>2013-04-23T08:06:00Z</o:Created>
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<o:LastSaved>2013-04-23T08:08:00Z</o:LastSaved>
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<o:Pages>5</o:Pages>
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<o:Words>1090</o:Words>
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<o:Characters>6218</o:Characters>
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<o:Characters>6217</o:Characters>
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<o:Lines>51</o:Lines>
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<o:Paragraphs>14</o:Paragraphs>
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<o:CharactersWithSpaces>7294</o:CharactersWithSpaces>
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<o:CharactersWithSpaces>7293</o:CharactersWithSpaces>
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<o:Version>14.00</o:Version>
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</o:DocumentProperties>
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<o:OfficeDocumentSettings>
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@@ -43,6 +43,9 @@ w\:* {behavior:url(#default#VML);}
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href="cyto_proposal_draft_files/colorschememapping.xml">
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<!--[if gte mso 9]><xml>
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<w:WordDocument>
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<w:View>Print</w:View>
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<w:SpellingState>Clean</w:SpellingState>
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<w:GrammarState>Clean</w:GrammarState>
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<w:TrackMoves>false</w:TrackMoves>
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<w:TrackFormatting/>
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<w:PunctuationKerning/>
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@@ -371,9 +374,8 @@ href="cyto_proposal_draft_files/colorschememapping.xml">
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panose-1:2 11 6 4 3 5 4 4 2 4;
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mso-font-charset:0;
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mso-generic-font-family:swiss;
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mso-font-format:other;
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mso-font-pitch:variable;
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mso-font-signature:3 0 0 0 1 0;}
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mso-font-signature:-520081665 -1073717157 41 0 66047 0;}
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/* Style Definitions */
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p.MsoNormal, li.MsoNormal, div.MsoNormal
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{mso-style-unhide:no;
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@@ -574,8 +576,7 @@ p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
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font-size:8.0pt;
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font-family:"Tahoma","sans-serif";
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mso-fareast-font-family:Calibri;
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mso-fareast-theme-font:minor-latin;
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mso-bidi-font-family:Tahoma;}
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mso-fareast-theme-font:minor-latin;}
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p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
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{mso-style-priority:1;
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mso-style-unhide:no;
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@@ -739,6 +740,12 @@ span.TitleChar
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mso-themeshade:191;
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letter-spacing:.25pt;
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mso-font-kerning:14.0pt;}
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span.SpellE
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{mso-style-name:"";
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mso-spl-e:yes;}
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span.GramE
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{mso-style-name:"";
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mso-gram-e:yes;}
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.MsoChpDefault
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{mso-style-type:export-only;
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mso-default-props:yes;
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@@ -1279,14 +1286,14 @@ div.WordSection1
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@list l8
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{mso-list-id:1624657255;
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mso-list-type:hybrid;
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mso-list-template-ids:1668440594 67698701 67698691 67698693 67698689 67698691 67698693 67698689 67698691 67698693;}
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mso-list-template-ids:-1479218694 67698689 67698691 67698693 67698689 67698691 67698693 67698689 67698691 67698693;}
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@list l8:level1
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{mso-level-number-format:bullet;
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mso-level-text:\F0FC;
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mso-level-text:\F0B7;
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mso-level-tab-stop:none;
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mso-level-number-position:left;
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text-indent:-.25in;
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font-family:Wingdings;}
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font-family:Symbol;}
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@list l8:level2
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{mso-level-number-format:bullet;
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mso-level-text:o;
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@@ -1717,15 +1724,15 @@ Cytoscape 3.0 file formats.</p>
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<p class=MsoNormal><span style='mso-spacerun:yes'> </span>The idea is based
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upon suggested Idea 19: JavaScript JSON convertors for graph file formats, but
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I would like to drop the word “graph” from it, because this project will
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support virtually all formats accepted by Cytoscape 3.0 .</p>
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support virtually all formats accepted by Cytoscape <span class=GramE>3.0 .</span></p>
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<h1>Synopsis:</h1>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>This project deals with the conversion of different graph
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and other <span style='mso-spacerun:yes'> </span>formats used in Cytoscape 3.0
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to Json used in cytoscape.js and vice versa. </p>
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and <span class=GramE>other <span style='mso-spacerun:yes'> </span>formats</span>
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used in Cytoscape 3.0 to Json used in cytoscape.js and vice versa. </p>
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<p class=MsoNormal>Cytoscape 3.0 accepts file formats like xgmml, graphml, gml,
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nnf, sif, xls, sif, csv whereas cytoscape.js currently accepts only json
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@@ -1742,13 +1749,14 @@ support import and export to all the formats mentioned earlier.</p>
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<p class=MsoNormal>The Cytoscape 3.0 file formats that will be supported are:</p>
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<p class=MsoNormal>Xgmml, Graphml, Sif, Nnf, Gml (,Csv, Xlsx).</p>
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<p class=MsoNormal>Xgmml, Graphml, Sif, Nnf, Gml (<span class=GramE>,Csv</span>,
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Xlsx).</p>
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<p class=MsoNormal>They are arranged according to their priority and so this is
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the order in which their json converters will be implemented. The last two (in
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bracket) will be kept as extras, meaning that they will be implemented only if
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the project is finished well before the deadline (see the timeline for details)
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.</p>
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the project is finished well before the deadline (see the timeline for details<span
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class=GramE>) .</span></p>
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<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
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id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
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@@ -1784,12 +1792,13 @@ alt="Description: C:\Users\Abhas_2\Desktop\cyto\cyto_proposal.png" v:shapes="Pic
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style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
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style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>
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</span></span></span><![endif]>Xgmml: This is the top priority format and hence
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will be dealt with first. Xml parsers available in native javascript and jquery
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will be used for parsing the xgmml file. Then some JavaScript code (using
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looping and if needed, regular expressions) will deal with the parsed xml file
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to convert them correctly into javascript variables and objects. Finally, they
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can be used to generate its json representation. (Maybe, take some inspiration
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from this library in Gremlin (written in java): <a
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will be dealt with first. Xml parsers available in native <span class=SpellE>javascript</span>
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and <span class=SpellE>jquery</span> will be used for parsing the xgmml file.
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Then some JavaScript code (using looping and if needed, regular expressions)
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will deal with the parsed xml file to convert them correctly into <span
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class=SpellE>javascript</span> variables and objects. Finally, they can be used
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to generate its json representation. (Maybe, take some inspiration from this
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library in Gremlin (written in java): <a
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href="https://github.com/tinkerpop/blueprints/wiki/GraphSON-Reader-and-Writer-Library">https://github.com/tinkerpop/blueprints/wiki/GraphSON-Reader-and-Writer-Library</a>
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)</p>
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@@ -1826,25 +1835,25 @@ Symbol'><span style='mso-list:Ignore'>
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style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
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style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>
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</span></span></span><![endif]>Graphml:<span style='mso-spacerun:yes'>
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</span>Graphml is also a xml-based format, so the implementation process is
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same as that of the previous one. Only the code will be different to take care
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of the syntax difference of these formats.</p>
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</span>Graphml is also <span class=GramE>a</span> xml-based format, so the
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implementation process is same as that of the previous one. Only the code will
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be different to take care of the syntax difference of these formats.</p>
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<p class=MsoListParagraphCxSpMiddle><o:p> </o:p></p>
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<p class=MsoListParagraphCxSpMiddle>Before<span style='mso-spacerun:yes'>
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</span>I move on to the other ones, here is a small chart for reference:</p>
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<p class=MsoListParagraphCxSpMiddle>Before I move on to the other ones, here is
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a small chart for reference:</p>
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<p class=MsoListParagraphCxSpLast><o:p> </o:p></p>
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<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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id="Picture_x0020_1" o:spid="_x0000_i1025" type="#_x0000_t75" alt="Description: C:\Users\Abhas_2\Desktop\cyto\cyto_implementation.png"
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style='width:467.25pt;height:272.25pt;visibility:visible;mso-wrap-style:square'>
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<p class=MsoListParagraphCxSpLast><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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id="Picture_x0020_3" o:spid="_x0000_i1025" type="#_x0000_t75" alt="Description: C:\Users\Abhas_2\Desktop\cyto\cyto_implementation.png"
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style='width:591.75pt;height:345pt;visibility:visible;mso-wrap-style:square'>
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<v:imagedata src="cyto_proposal_draft_files/image003.png" o:title="cyto_implementation"/>
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</v:shape><![endif]--><![if !vml]><img border=0 width=623 height=363
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src="cyto_proposal_draft_files/image004.jpg"
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</v:shape><![endif]--><![if !vml]><img border=0 width=789 height=460
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src="cyto_proposal_draft_files/image003.png"
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alt="Description: C:\Users\Abhas_2\Desktop\cyto\cyto_implementation.png"
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v:shapes="Picture_x0020_1"><![endif]></span></p>
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v:shapes="Picture_x0020_3"><![endif]></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l7 level1 lfo2'><![if !supportLists]><span
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style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
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@@ -1855,15 +1864,16 @@ implementation of these converters (written by me) available at <a
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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
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</a><span style='mso-spacerun:yes'> </span>. Nnf files will be stripped off its
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network information and treated just like a Sif file (Possible problem with
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multi-network files ??)</p>
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multi-network <span class=GramE>files ??)</span></p>
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<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l7 level1 lfo2'><![if !supportLists]><span
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style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
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style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>
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</span></span></span><![endif]>GML:<span style='mso-spacerun:yes'> </span>A
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custom-made parser needs to be built based on regular expressions (native js or
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possibly using xregexp library <a href="http://xregexp.com/">http://xregexp.com/</a>
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). The rest of the plan is the same as that of xgmml, only this new parser will
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custom-made parser needs to be built based on regular expressions (native <span
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class=SpellE>js</span> or possibly using xregexp library <a
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href="http://xregexp.com/">http://xregexp.com/</a> ). The rest of the plan is
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the same as that of <span class=GramE>xgmml,</span> only this new parser will
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be used.</p>
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<p class=MsoNormal>Few words on the extras:</p>
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@@ -1894,7 +1904,7 @@ called Xlsx.js <a href="https://github.com/stephen-hardy/xlsx.js">https://github
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. I am not much sure if I can pull off this part, but I am still including this
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in the proposal mostly for my inspiration than anything else. Also, I know that
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the Cytoscape project originally supported .xls, but I think its best kept to
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Microsoft Excel for converting .xls into .xlsx .</p>
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Microsoft Excel for converting .xls into .<span class=GramE>xlsx .</span></p>
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<p class=MsoNormal><o:p> </o:p></p>
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@@ -1986,7 +1996,8 @@ tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
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mso-bidi-font-size:11.0pt;line-height:115%;mso-bidi-font-family:Calibri;
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mso-bidi-theme-font:minor-latin'><span style='mso-list:Ignore'>5.<span
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style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span
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style='mso-spacerun:yes'> </span>July 26 – July 28 (3 days): Test graphml converter</p>
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style='mso-spacerun:yes'> </span>July 26 – July 28 (3 days): Test graphml
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converter</p>
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<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l10 level1 lfo9;
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tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
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@@ -2002,7 +2013,7 @@ mso-bidi-font-size:11.0pt;line-height:115%;mso-bidi-font-family:Calibri;
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mso-bidi-theme-font:minor-latin'><span style='mso-list:Ignore'>7.<span
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style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>July
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30: Take a day off from coding and analyze what went right and wrong in the
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first-term. (How about a blog post? :D)</p>
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first-term. (How about a blog post<span class=GramE>? :</span>D)</p>
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<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l10 level1 lfo9;
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tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
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@@ -2079,16 +2090,16 @@ mso-bidi-font-size:11.0pt;line-height:115%;mso-bidi-font-family:Calibri;
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mso-bidi-theme-font:minor-latin'><span style='mso-list:Ignore'>3.<span
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style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>The
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input graph formats might not be well-formed (if manually created). (Maybe, add
|
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a xml-checker and discard non well-formed files. Such a checker might not be
|
||||
possible in case of non-xml based formats. )</p>
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<span class=GramE>a</span> xml-checker and discard non well-formed files. Such
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||||
a checker might not be possible in case of non-xml based formats. )</p>
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<h1>What can I bring to the team?</h1>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l8 level1 lfo14'><![if !supportLists]><span
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style='font-family:Wingdings;mso-fareast-font-family:Wingdings;mso-bidi-font-family:
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Wingdings'><span style='mso-list:Ignore'>ü<span style='font:7.0pt "Times New Roman"'>
|
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style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
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Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span></span><![endif]>Yes, I am committed in working hard for this
|
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GSOC project this summer. <span style='mso-spacerun:yes'> </span>I do not have
|
||||
any other commitment during the summer other than my college internals for the
|
||||
@@ -2097,17 +2108,17 @@ September. I am not yet sure about the date, but I will ask for a one-week
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||||
break during that time. I hope it won’t be much of a problem.</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l8 level1 lfo14'><![if !supportLists]><span
|
||||
style='font-family:Wingdings;mso-fareast-font-family:Wingdings;mso-bidi-font-family:
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||||
Wingdings'><span style='mso-list:Ignore'>ü<span style='font:7.0pt "Times New Roman"'>
|
||||
style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
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Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span></span><![endif]>Being my first GSOC project, I am also
|
||||
super-excited about it, can’t wait to have a fruitful summer this year.</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l8 level1 lfo14'><![if !supportLists]><span
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||||
style='font-family:Wingdings;mso-fareast-font-family:Wingdings;mso-bidi-font-family:
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||||
Wingdings'><span style='mso-list:Ignore'>ü<span style='font:7.0pt "Times New Roman"'>
|
||||
style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
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||||
Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span></span><![endif]>I wish to learn some more about the core
|
||||
Cytoscape project but as I am not a Java developer, I wish to linger with the
|
||||
Cytoscape.js project.</p>
|
||||
Cytoscape project but as I am not a Java <span class=GramE>developer,</span> I
|
||||
wish to linger with the Cytoscape.js project.</p>
|
||||
|
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</div>
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@@ -5,6 +5,5 @@
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<o:File HRef="image001.png"/>
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<o:File HRef="image002.png"/>
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<o:File HRef="image003.png"/>
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<o:File HRef="image004.jpg"/>
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<o:File HRef="filelist.xml"/>
|
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</xml>
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