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bendtherules
2013-05-01 04:13:33 +05:30
parent 504d34e671
commit fb1d141ac0
1 changed files with 155 additions and 127 deletions
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@@ -22,16 +22,16 @@ w\:* {behavior:url(#default#VML);}
<o:DocumentProperties> <o:DocumentProperties>
<o:Author>Abhas Bhattacharya</o:Author> <o:Author>Abhas Bhattacharya</o:Author>
<o:LastAuthor>Abhas Bhattacharya</o:LastAuthor> <o:LastAuthor>Abhas Bhattacharya</o:LastAuthor>
<o:Revision>7</o:Revision> <o:Revision>8</o:Revision>
<o:TotalTime>44</o:TotalTime> <o:TotalTime>45</o:TotalTime>
<o:Created>2013-04-23T21:30:00Z</o:Created> <o:Created>2013-04-23T21:30:00Z</o:Created>
<o:LastSaved>2013-04-30T21:31:00Z</o:LastSaved> <o:LastSaved>2013-04-30T22:41:00Z</o:LastSaved>
<o:Pages>5</o:Pages> <o:Pages>5</o:Pages>
<o:Words>1901</o:Words> <o:Words>1911</o:Words>
<o:Characters>10836</o:Characters> <o:Characters>10899</o:Characters>
<o:Lines>90</o:Lines> <o:Lines>90</o:Lines>
<o:Paragraphs>25</o:Paragraphs> <o:Paragraphs>25</o:Paragraphs>
<o:CharactersWithSpaces>12712</o:CharactersWithSpaces> <o:CharactersWithSpaces>12785</o:CharactersWithSpaces>
<o:Version>14.00</o:Version> <o:Version>14.00</o:Version>
</o:DocumentProperties> </o:DocumentProperties>
<o:OfficeDocumentSettings> <o:OfficeDocumentSettings>
@@ -43,6 +43,8 @@ w\:* {behavior:url(#default#VML);}
href="cyto_proposal_draft_files/colorschememapping.xml"> href="cyto_proposal_draft_files/colorschememapping.xml">
<!--[if gte mso 9]><xml> <!--[if gte mso 9]><xml>
<w:WordDocument> <w:WordDocument>
<w:SpellingState>Clean</w:SpellingState>
<w:GrammarState>Clean</w:GrammarState>
<w:TrackMoves>false</w:TrackMoves> <w:TrackMoves>false</w:TrackMoves>
<w:TrackFormatting/> <w:TrackFormatting/>
<w:PunctuationKerning/> <w:PunctuationKerning/>
@@ -552,7 +554,8 @@ p.MsoTitleCxSpLast, li.MsoTitleCxSpLast, div.MsoTitleCxSpLast
letter-spacing:.25pt; letter-spacing:.25pt;
mso-font-kerning:14.0pt;} mso-font-kerning:14.0pt;}
a:link, span.MsoHyperlink a:link, span.MsoHyperlink
{mso-style-priority:99; {mso-style-noshow:yes;
mso-style-priority:99;
color:blue; color:blue;
mso-themecolor:hyperlink; mso-themecolor:hyperlink;
text-decoration:underline; text-decoration:underline;
@@ -746,6 +749,12 @@ span.BalloonTextChar
mso-ascii-font-family:Tahoma; mso-ascii-font-family:Tahoma;
mso-hansi-font-family:Tahoma; mso-hansi-font-family:Tahoma;
mso-bidi-font-family:Tahoma;} mso-bidi-font-family:Tahoma;}
span.SpellE
{mso-style-name:"";
mso-spl-e:yes;}
span.GramE
{mso-style-name:"";
mso-gram-e:yes;}
.MsoChpDefault .MsoChpDefault
{mso-style-type:export-only; {mso-style-type:export-only;
mso-default-props:yes; mso-default-props:yes;
@@ -1208,9 +1217,9 @@ mso-border-bottom-themecolor:accent1;padding:0in 0in 4.0pt 0in'>
Cytoscape 3.0 file formats.</p> Cytoscape 3.0 file formats.</p>
<p class=MsoNormal><span style='mso-spacerun:yes'> </span>The idea is based <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 I upon suggested Idea 19: JavaScript JSON convertors for graph file formats, but
would like to drop the word “graph” from it, because this project will support I would like to drop the word “graph” from it, because this project will
virtually all formats accepted by Cytoscape 3.0 .</p> support virtually all formats accepted by Cytoscape <span class=GramE>3.0 .</span></p>
<h1>Synopsis:</h1> <h1>Synopsis:</h1>
@@ -1233,13 +1242,14 @@ generation of json representation.</p>
<p class=MsoNormal>The Cytoscape 3.0 file formats that will be supported are:</p> <p class=MsoNormal>The Cytoscape 3.0 file formats that will be supported are:</p>
<p class=MsoNormal>Xgmml, Graphml, Sif, Nnf, Gml (,Csv, Xlsx).</p> <p class=MsoNormal>Xgmml, Graphml, Sif, Nnf, Gml (<span class=GramE>,Csv</span>,
Xlsx).</p>
<p class=MsoNormal>They are arranged according to their priority and so this is <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 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 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) the project is finished well before the deadline (see the timeline for details<span
.</p> class=GramE>) .</span></p>
<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype <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" id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
@@ -1262,12 +1272,12 @@ the project is finished well before the deadline (see the timeline for details)
<v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/> <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
<o:lock v:ext="edit" aspectratio="t"/> <o:lock v:ext="edit" aspectratio="t"/>
</v:shapetype><v:shape id="Picture_x0020_2" o:spid="_x0000_i1026" type="#_x0000_t75" </v:shapetype><v:shape id="Picture_x0020_2" o:spid="_x0000_i1026" type="#_x0000_t75"
alt="Description: Description: Description: C:\Users\Abhas_2\Desktop\cyto\cyto_proposal.png" alt="Description: Description: Description: Description: C:\Users\Abhas_2\Desktop\cyto\cyto_proposal.png"
style='width:468pt;height:312pt;visibility:visible;mso-wrap-style:square'> 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:imagedata src="cyto_proposal_draft_files/image001.png" o:title="cyto_proposal"/>
</v:shape><![endif]--><![if !vml]><img width=624 height=416 </v:shape><![endif]--><![if !vml]><img width=624 height=416
src="cyto_proposal_draft_files/image001.png" src="cyto_proposal_draft_files/image001.png"
alt="Description: Description: Description: C:\Users\Abhas_2\Desktop\cyto\cyto_proposal.png" alt="Description: Description: Description: Description: C:\Users\Abhas_2\Desktop\cyto\cyto_proposal.png"
v:shapes="Picture_x0020_2"><![endif]></span></p> v:shapes="Picture_x0020_2"><![endif]></span></p>
<p class=MsoNormal>Now, this is how I plan to deal with each of them.</p> <p class=MsoNormal>Now, this is how I plan to deal with each of them.</p>
@@ -1276,12 +1286,13 @@ v:shapes="Picture_x0020_2"><![endif]></span></p>
style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><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; 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 </span></span></span><![endif]>Xgmml: This is the top priority format and hence
will be dealt with first. Xml parsers available in native javascript and jquery will be dealt with first. Xml parsers available in native <span class=SpellE>javascript</span>
will be used for parsing the xgmml file. Then some JavaScript code (using and <span class=SpellE>jquery</span> will be used for parsing the xgmml file.
looping and if needed, regular expressions) will deal with the parsed xml file Then some JavaScript code (using looping and if needed, regular expressions)
to convert them correctly into javascript variables and objects. Finally, they will deal with the parsed xml file to convert them correctly into <span
can be used to generate its json representation. (Maybe, take some inspiration class=SpellE>javascript</span> variables and objects. Finally, they can be used
from this library in Gremlin (written in java): <a to generate its json representation. (Maybe, take some inspiration from this
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> 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> )</p>
@@ -1319,8 +1330,9 @@ Symbol'><span style='mso-list:Ignore'>
text-indent:-.25in;mso-list:l0 level2 lfo6'><![if !supportLists]><span 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-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; 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 a “edge” is </span></span></span><![endif]>Whether it is a “node” or <span class=GramE>a</span>
represented by “group” in json. All its data is stored in the “data” object.</p> “edge” is represented by “group” in json. All its data is stored in the “data”
object.</p>
<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
auto;text-indent:-.25in;mso-list:l0 level2 lfo6'><![if !supportLists]><span auto;text-indent:-.25in;mso-list:l0 level2 lfo6'><![if !supportLists]><span
@@ -1342,9 +1354,9 @@ 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-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; style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></span><![endif]>The &lt;att&gt; tags without a “value” attribute </span></span></span><![endif]>The &lt;att&gt; tags without a “value” attribute
are considered as objects and its sub-tags and attributes are considered as properties are considered as objects and its sub-tags and attributes are considered as
of that object. These sub-tags and attributes are then converted in accordance properties of that object. These sub-tags and attributes are then converted in
with the previous rules.</p> accordance with the previous rules.</p>
<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto; <p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
text-indent:-.25in;mso-list:l0 level2 lfo6'><![if !supportLists]><span text-indent:-.25in;mso-list:l0 level2 lfo6'><![if !supportLists]><span
@@ -1389,19 +1401,18 @@ style='mso-spacerun:yes'>
<p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span <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; style='mso-spacerun:yes'>    </span>&lt;graphics width=&quot;1&quot;
fill=&quot;#fcfffd&quot;&gt;<o:p></o:p></span></p> fill=&quot;#<span class=SpellE>fcfffd</span>&quot;&gt;<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-spacerun:yes'>        </span>&lt;att style='mso-spacerun:yes'>        </span>&lt;att name=&quot;<span class=SpellE>cytoscapeNodeGraphicsAttributes</span>&quot;&gt;<o:p></o:p></span></p>
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 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-spacerun:yes'>            </span>&lt;att style='mso-spacerun:yes'>            </span>&lt;att name=&quot;<span
name=&quot;nodeTransparency&quot; value=&quot;1.0&quot;/&gt;<o:p></o:p></span></p> class=SpellE>nodeTransparency</span>&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 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-spacerun:yes'>            </span>&lt;att style='mso-spacerun:yes'>            </span>&lt;att name=&quot;<span
name=&quot;nodeLabelFont&quot; value=&quot;Default-0-12&quot;/&gt;<o:p></o:p></span></p> class=SpellE>nodeLabelFont</span>&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 <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> style='mso-spacerun:yes'>        </span>&lt;/att&gt;<o:p></o:p></span></p>
@@ -1422,46 +1433,46 @@ 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"'>[<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-spacerun:yes'>    </span>{ “data”: {<o:p></o:p></span></p> style='mso-spacerun:yes'>    </span><span class=GramE>{ “</span>data”: {<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-spacerun:yes'>                style='mso-spacerun:yes'>                </span>&quot;<span class=GramE>id</span>&quot;:&quot;YKR026C&quot;,<o:p></o:p></span></p>
</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 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-spacerun:yes'>                style='mso-spacerun:yes'>                </span>&quot;<span class=GramE>label</span>&quot;:&quot;YBR043C&quot;,<o:p></o:p></span></p>
</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 <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> 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 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-spacerun:yes'>                </span>&quot;GO Cellular style='mso-spacerun:yes'>                </span>&quot;GO Cellular
Component&quot;:[&quot;cell&quot;, &quot;cell part&quot;],<o:p></o:p></span></p> Component&quot;<span class=GramE>:[</span>&quot;cell&quot;, &quot;cell
part&quot;],<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-spacerun:yes'>                style='mso-spacerun:yes'>              </span><span
</span>&quot;graphics&quot;:{&quot;width&quot;:&quot;1&quot;,<o:p></o:p></span></p> style='mso-spacerun:yes'>  </span>&quot;<span class=GramE>graphics</span>&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 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-spacerun:yes'>                            style='mso-spacerun:yes'>                            </span>&quot;<span
</span>&quot;fill&quot;:&quot;#fcfffd&quot;,<o:p></o:p></span></p> class=GramE>fill</span>&quot;:&quot;#<span class=SpellE>fcfffd</span>&quot;,<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span <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>&quot;<span
style='mso-spacerun:yes'>                         </span>&quot;cytoscapeNodeGraphicsAttributes&quot;:{<o:p></o:p></span></p> class=SpellE><span class=GramE>cytoscapeNodeGraphicsAttributes</span></span>&quot;:{<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-spacerun:yes'>                                                                style='mso-spacerun:yes'>                                                               
</span>&quot;nodeTransparency&quot;:&quot;1.0&quot;,<o:p></o:p></span></p> </span>&quot;<span class=GramE>nodeTransparency</span>&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 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-spacerun:yes'>                                                                style='mso-spacerun:yes'>                             </span><span
</span>&quot;nodeLabelFont&quot;:&quot;Default-0-12&quot;<o:p></o:p></span></p> style='mso-spacerun:yes'>                                   </span>&quot;<span
class=GramE>nodeLabelFont</span>&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 <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'>                                                             
style='mso-spacerun:yes'>                                                    </span>}<o:p></o:p></span></p> </span>}<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span <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> style='mso-spacerun:yes'>                            </span>}<o:p></o:p></span></p>
@@ -1470,7 +1481,8 @@ style='mso-spacerun:yes'>
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 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-spacerun:yes'>      </span>&quot;group&quot;: &quot;nodes&quot;<o:p></o:p></span></p> style='mso-spacerun:yes'>      </span>&quot;<span class=GramE>group</span>&quot;:
&quot;nodes&quot;<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span <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> style='mso-spacerun:yes'>    </span>}<o:p></o:p></span></p>
@@ -1483,9 +1495,9 @@ style='mso-spacerun:yes'>
style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span 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; 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></span></span><![endif]>Graphml:<span style='mso-spacerun:yes'> 
</span>Graphml is also a xml-based format, so the implementation process is </span>Graphml is also <span class=GramE>a</span> xml-based format, so the
same as that of the previous one. Only the code will be different to take care implementation process is same as that of the previous one. Only the code will
of the syntax difference of these formats.</p> be different to take care of the syntax difference of these formats.</p>
<p class=MsoNormal style='margin-left:.5in'>Conversion guideline:</p> <p class=MsoNormal style='margin-left:.5in'>Conversion guideline:</p>
@@ -1493,7 +1505,8 @@ of the syntax difference of these formats.</p>
text-indent:-.25in;mso-list:l0 level2 lfo6'><![if !supportLists]><span 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-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; 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 ( <a </span></span></span><![endif]>Make use of the graphml – attribute values <span
class=GramE>( </span><a
href="http://graphml.graphdrawing.org/primer/graphml-primer.html#AttributesValues">http://graphml.graphdrawing.org/primer/graphml-primer.html#AttributesValues</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> ) to know the attribute type and the default values, if present.</p>
@@ -1503,13 +1516,14 @@ 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; 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></span></span><![endif]>All the<span style='mso-spacerun:yes'> 
</span>“key” attributes in the &lt;data&gt; tags will be converted into json </span>“key” attributes in the &lt;data&gt; tags will be converted into json
data of type “attr.type” (which are provided as graphml – attribute values )</p> data of type “<span class=SpellE>attr.type</span>” (which are provided as
graphml – attribute values )</p>
<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
auto;text-indent:-.25in;mso-list:l0 level2 lfo6'><![if !supportLists]><span 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-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; 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 ( <a </span></span></span><![endif]>Convert complex types <span class=GramE>( </span><a
href="http://graphml.graphdrawing.org/primer/graphml-primer.html#Complex">http://graphml.graphdrawing.org/primer/graphml-primer.html#Complex</a> href="http://graphml.graphdrawing.org/primer/graphml-primer.html#Complex">http://graphml.graphdrawing.org/primer/graphml-primer.html#Complex</a>
) into objects.</p> ) into objects.</p>
@@ -1525,7 +1539,7 @@ do-able.)</p>
<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p> <p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
<p class=MsoListParagraphCxSpMiddle>[Side-by-side examples are not provided for <p class=MsoListParagraphCxSpMiddle>[Side-by-side examples are not provided for
this one, as they are pretty easy to understand. ]</p> this one, as they are pretty easy to understand<span class=GramE>. ]</span></p>
<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p> <p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
@@ -1535,12 +1549,12 @@ this one, as they are pretty easy to understand. ]</p>
a small chart for reference:</p> a small chart for reference:</p>
<p class=MsoListParagraphCxSpLast><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape <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: 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: Description: C:\Users\Abhas_2\Desktop\cyto\cyto_implementation.png"
style='width:591.75pt;height:345pt;visibility:visible;mso-wrap-style:square'> style='width:591.75pt;height:345pt;visibility:visible;mso-wrap-style:square'>
<v:imagedata src="cyto_proposal_draft_files/image002.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 </v:shape><![endif]--><![if !vml]><img border=0 width=789 height=460
src="cyto_proposal_draft_files/image002.png" src="cyto_proposal_draft_files/image002.png"
alt="Description: Description: Description: C:\Users\Abhas_2\Desktop\cyto\cyto_implementation.png" alt="Description: Description: Description: Description: C:\Users\Abhas_2\Desktop\cyto\cyto_implementation.png"
v:shapes="Picture_x0020_3"><![endif]></span></p> v:shapes="Picture_x0020_3"><![endif]></span></p>
<p class=MsoNormal><o:p>&nbsp;</o:p></p> <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1548,8 +1562,8 @@ v:shapes="Picture_x0020_3"><![endif]></span></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo6'><![if !supportLists]><span <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-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; 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 written </span></span></span><![endif]>Sif and Nnf: Very simple jS code needs to be
to take care of these file formats. There is already a python-based written to take care of these file formats. There is already a python-based
implementation of these converters (written by me) available at <a 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 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; </a><span style='mso-spacerun:yes'> </span>. <span style='background:lightgrey;
@@ -1562,9 +1576,10 @@ 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-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; 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 </span></span></span><![endif]>GML:<span style='mso-spacerun:yes'>  </span>A
custom-made parser needs to be built based on regular expressions (native js or custom-made parser needs to be built based on regular expressions (native <span
possibly using xregexp library <a href="http://xregexp.com/">http://xregexp.com/</a> class=SpellE>js</span> or possibly using xregexp library <a
). The rest of the plan is the same as that of xgmml, only this new parser will href="http://xregexp.com/">http://xregexp.com/</a> ). The rest of the plan is
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 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 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> tags are not present here, everything is separated by space/tab).</p>
@@ -1573,37 +1588,40 @@ 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; <p class=MsoNormal style='margin-left:.5in'><span style='font-size:14.0pt;
line-height:115%;background:aqua;mso-highlight:aqua'>GML</span><span line-height:115%;background:aqua;mso-highlight:aqua'>GML</span><span
style='font-size:14.0pt;line-height:115%'> ( <a style='font-size:14.0pt;line-height:115%'> <span class=GramE>( </span><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> 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> )<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'>node<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:.5in'><span class=GramE><span
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"'>[<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><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><span class=GramE>id</span><span
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 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-tab-count:1'>            </span>label<span style='mso-tab-count: style='mso-tab-count:1'>            </span><span class=GramE>label</span><span
1'>     </span>&quot;YKR026C&quot;<o:p></o:p></span></p> style='mso-tab-count: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 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-tab-count:1'>            </span>graphics<o:p></o:p></span></p> style='mso-tab-count:1'>            </span><span class=GramE>graphics</span><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span <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> 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 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-tab-count:2'>                        </span>x<span style='mso-tab-count: style='mso-tab-count:2'>                        </span><span class=GramE>x</span><span
1'>          </span>1916.0<o:p></o:p></span></p> style='mso-tab-count: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 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-tab-count:2'>                        </span>type<span style='mso-tab-count:2'>                        </span><span class=GramE>type</span><span
style='mso-tab-count:1'>     </span>&quot;ellipse&quot;<o:p></o:p></span></p> 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 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-tab-count:2'>                        </span>fill<span style='mso-tab-count:2'>                        </span><span class=GramE>fill</span><span
style='mso-tab-count:1'>         </span>&quot;#E1E1E1&quot;<o:p></o:p></span></p> 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 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
@@ -1623,25 +1641,24 @@ 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"'>[<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-spacerun:yes'>    </span>{ data: {<o:p></o:p></span></p> style='mso-spacerun:yes'>    </span><span class=GramE>{ data</span>: {<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-spacerun:yes'>                </span>&quot;id&quot;:0,<o:p></o:p></span></p> style='mso-spacerun:yes'>                </span>&quot;<span class=GramE>id</span>&quot;:0,<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-spacerun:yes'>                style='mso-spacerun:yes'>                </span>&quot;<span class=GramE>label</span>&quot;:&quot;YKR026C&quot;,<o:p></o:p></span></p>
</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 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-spacerun:yes'>                style='mso-spacerun:yes'>                </span>&quot;<span class=GramE>graphics</span>&quot;:{&quot;x&quot;:1916.0,<o:p></o:p></span></p>
</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 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-spacerun:yes'>                            </span>&quot;type&quot;:&quot;ellipse&quot;,<o:p></o:p></span></p> style='mso-spacerun:yes'>                            </span>&quot;<span
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 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-spacerun:yes'>                            style='mso-spacerun:yes'>                            </span>&quot;<span
</span>&quot;fill&quot;:&quot;#E1E1E1&quot;,<o:p></o:p></span></p> class=GramE>fill</span>&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 <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> style='mso-spacerun:yes'>                            </span>}<o:p></o:p></span></p>
@@ -1650,7 +1667,8 @@ style='mso-spacerun:yes'>
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 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span
style='mso-spacerun:yes'>      </span>&quot;group&quot;: &quot;nodes&quot;<o:p></o:p></span></p> style='mso-spacerun:yes'>      </span>&quot;<span class=GramE>group</span>&quot;:
&quot;nodes&quot;<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in'><span style='font-family:"Arial","sans-serif"'><span <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> style='mso-spacerun:yes'>    </span>}<o:p></o:p></span></p>
@@ -1661,14 +1679,15 @@ style='mso-spacerun:yes'>
<p class=MsoNormal>Few words on the extras:</p> <p class=MsoNormal>Few words on the extras:</p>
<p class=MsoNormal>These extras will be done only if there is ample time left after <p class=MsoNormal>These extras will be done only if there is ample time left
the completion of the whole project, so there is no way that they will harm the after the completion of the whole project, so there is no way that they will
main project. I am aware that new GSOC applicants like me tend to propose a lot harm the main project. I am aware that new GSOC applicants like me tend to
more than they can actually complete, so I have tried not to fall in that trap. propose a lot more than they can actually complete, so I have tried not to fall
But these extras are here, because I plan to do them in the future, within or in that trap. But these extras are here, because I plan to do them in the
after GSOC.<span style='mso-spacerun:yes'>  </span>Also, as a side note, in future, within or after GSOC.<span style='mso-spacerun:yes'>  </span>Also, as a
future, I wish to release this codes as a separate jS library for converting side note, in future, I wish to release this codes as a separate jS library for
customized-xml formats into json (I hope my mentoring org will allow this).</p> converting customized-xml formats into json (I hope my mentoring org will allow
this).</p>
<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l0 level1 lfo6'><![if !supportLists]><span <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 style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
@@ -1681,14 +1700,14 @@ 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; 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; </span></span></span><![endif]>Xlsx: <span style='color:red;background:lightgrey;
mso-highlight:lightgrey'>**Potential License Issue**</span><span mso-highlight:lightgrey'>**Potential License Issue**</span><span
style='color:red'> </span>This is the most challenging part. I wouldn’t have style='color:red'> </span><span class=GramE>This</span> is the most challenging
tried this if there was no cross-browser external library to read and write part. I wouldn’t have tried this if there was no cross-browser external library
xlsx format. But thankfully and quite surprisingly, there is one called Xlsx.js to read and write xlsx format. But thankfully and quite surprisingly, there is
<a href="https://github.com/stephen-hardy/xlsx.js">https://github.com/stephen-hardy/xlsx.js</a> one called Xlsx.js <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 . 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 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 the Cytoscape project originally supported .xls, but I think its best kept to
Microsoft Excel for converting .xls into .xlsx .</p> Microsoft Excel for converting .xls into .<span class=GramE>xlsx .</span></p>
<p class=MsoNormal><o:p>&nbsp;</o:p></p> <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1797,7 +1816,7 @@ 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 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 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 30: Take a day off from coding and analyze what went right and wrong in the
first-term. (How about a blog post? :D)</p> first-term. (How about a blog post<span class=GramE>? :</span>D)</p>
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo8; <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo8;
tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt; tab-stops:list .5in'><![if !supportLists]><span style='font-size:10.0pt;
@@ -1845,8 +1864,8 @@ 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 4 – September 16 (13 days): Buffer time (If everything is working, work on the
extras) </p> extras) </p>
<p class=MsoNormal>(Feedback will be obtained for all the converters from the community <p class=MsoNormal>(Feedback will be obtained for all the converters from the
and they will be given more importance than the extras)</p> community and they will be given more importance than the extras)</p>
<h1>Possible hurdles:</h1> <h1>Possible hurdles:</h1>
@@ -1874,8 +1893,8 @@ 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 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 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 input graph formats might not be well-formed (if manually created). (Maybe, add
a xml-checker and discard non well-formed files. Such a checker might not be <span class=GramE>a</span> xml-checker and discard non well-formed files. Such
possible in case of non-xml based formats. )</p> a checker might not be possible in case of non-xml based formats. )</p>
<h1>What can I bring to the team?</h1> <h1>What can I bring to the team?</h1>
@@ -1901,8 +1920,8 @@ super-excited about it, can
style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family: 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; 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 </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 project but as I am not a Java <span class=GramE>developer,</span> I
Cytoscape.js project.</p> wish to linger with the Cytoscape.js project.</p>
<p class=MsoNormal><o:p>&nbsp;</o:p></p> <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1910,47 +1929,56 @@ Cytoscape.js project.</p>
<p class=MsoNormal><o:p>&nbsp;</o:p></p> <p class=MsoNormal><o:p>&nbsp;</o:p></p>
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Name:</b> Abhas <p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Name:</b> <span
Bhattacharya</p> class=SpellE>Abhas</span> Bhattacharya</p>
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Email:</b> <span <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> 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 <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 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> BESU <span class=GramE>( </span><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 <p class=MsoNormal><span class=GramE><b style='mso-bidi-font-weight:normal'>Programming
of choice:</b> Python, Javascript, C, C++, Java (little).</p> Languages of choice:</b> Python, <span class=SpellE>Javascript</span>, C, C++,
Java (little).</span></p>
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Related programming
knowledge: </b>Regular expressions, <span class=SpellE>jQuery</span>, Xml
Parsing.</p>
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Prior experience with <p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Prior experience with
open source development:<o:p></o:p></b></p> open source development:<o:p></o:p></b></p>
<p class=MsoNormal>I have some experience in working with Git and playing <p class=MsoNormal>I have some experience in working with <span class=SpellE>Git</span>
around with forked projects, but didn’t really contribute in them.</p> 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 <p class=MsoNormal>Mostly, I am into game development, with <span class=GramE>python
and javascript.</p> ,</span> <span class=SpellE>gamemaker</span> and <span class=SpellE>javascript</span>.</p>
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>What do I want to <p class=MsoNormal><b style='mso-bidi-font-weight:normal'>What do I want to
learn this summer?<o:p></o:p></b></p> learn this summer?<o:p></o:p></b></p>
<p class=MsoNormal>It will be a great opportunity for me to contribute to a <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. project like Cytoscape by developing these converters which should help
Being mostly a hobby developer, I want to learn how to collaborate and code on end-users. Being mostly a hobby developer, I want to learn how to collaborate
real-life open-source projects.</p> and code on real-life open-source projects.</p>
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Any prior exposure to <p class=MsoNormal><span class=GramE><b style='mso-bidi-font-weight:normal'>Any
biology or bioinformatics?<o:p></o:p></b></p> prior exposure to biology or bioinformatics?</b></span><b style='mso-bidi-font-weight:
normal'><o:p></o:p></b></p>
<p class=MsoNormal>Studied biology till the 10<sup>th</sup> grade.</p> <p class=MsoNormal><span class=GramE>Studied biology till the 10<sup>th</sup>
grade.</span></p>
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'>Any interest in <p class=MsoNormal><span class=GramE><b style='mso-bidi-font-weight:normal'>Any
learning a bit of biology this summer?<o:p></o:p></b></p> interest in learning a bit of biology this summer?</b></span><b
style='mso-bidi-font-weight:normal'><o:p></o:p></b></p>
<p class=MsoNormal>Sure. As I was asking around in the google groups, I would <p class=MsoNormal>Sure. As I was asking around in the <span class=SpellE>google</span>
like to know more about the working of the core Cytoscape project and also a groups, I would like to know more about the working of the core Cytoscape
little biology, whenever required.</p> project and also a little biology, whenever required.</p>
<p class=MsoNormal>** End **</p> <p class=MsoNormal>** End **</p>