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bendtherules
2013-05-01 03:03:00 +05:30
parent ce4f4092df
commit 504d34e671
4 changed files with 155 additions and 159 deletions
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@@ -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:TotalTime>11</o:TotalTime>
<o:Revision>7</o:Revision>
<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:Characters>9836</o:Characters>
<o:Lines>81</o:Lines>
<o:Paragraphs>23</o:Paragraphs>
<o:CharactersWithSpaces>11538</o:CharactersWithSpaces>
<o:Words>1901</o:Words>
<o:Characters>10836</o:Characters>
<o:Lines>90</o:Lines>
<o:Paragraphs>25</o:Paragraphs>
<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>
<w:WordDocument>
<w:SpellingState>Clean</w:SpellingState>
<w:GrammarState>Clean</w:GrammarState>
<w:TrackMoves>false</w:TrackMoves>
<w:TrackFormatting/>
<w:PunctuationKerning/>
@@ -67,6 +65,7 @@ href="cyto_proposal_draft_files/colorschememapping.xml">
<w:DontFlipMirrorIndents/>
<w:OverrideTableStyleHps/>
</w:Compatibility>
<w:BrowserLevel>MicrosoftInternetExplorer4</w:BrowserLevel>
<m:mathPr>
<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;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{mso-style-unhide:no;
@@ -576,8 +574,7 @@ p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
font-size:8.0pt;
font-family:"Tahoma","sans-serif";
mso-fareast-font-family:Calibri;
mso-fareast-theme-font:minor-latin;
mso-bidi-font-family:Tahoma;}
mso-fareast-theme-font:minor-latin;}
p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
{mso-style-priority:1;
mso-style-unhide:no;
@@ -749,12 +746,6 @@ span.BalloonTextChar
mso-ascii-font-family:Tahoma;
mso-hansi-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
{mso-style-type:export-only;
mso-default-props:yes;
@@ -1159,38 +1150,6 @@ div.WordSection1
text-indent:-.25in;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
@list l4:level2 lfo8
{mso-level-start-at:0;}
@list l4:level3 lfo8
{mso-level-start-at:0;}
@list l4:level4 lfo8
{mso-level-start-at:0;}
@list l4:level5 lfo8
{mso-level-start-at:0;}
@list l4:level6 lfo8
{mso-level-start-at:0;}
@list l4:level7 lfo8
{mso-level-start-at:0;}
@list l4:level8 lfo8
{mso-level-start-at:0;}
@list l4:level9 lfo8
{mso-level-start-at:0;}
@list l5:level2 lfo10
{mso-level-start-at:0;}
@list l5:level3 lfo10
{mso-level-start-at:0;}
@list l5:level4 lfo10
{mso-level-start-at:0;}
@list l5:level5 lfo10
{mso-level-start-at:0;}
@list l5:level6 lfo10
{mso-level-start-at:0;}
@list l5:level7 lfo10
{mso-level-start-at:0;}
@list l5:level8 lfo10
{mso-level-start-at:0;}
@list l5:level9 lfo10
{mso-level-start-at:0;}
ol
{margin-bottom:0in;}
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
I would like to drop the word “graph” from it, because this project will
support virtually all formats accepted by Cytoscape <span class=GramE>3.0 .</span></p>
upon suggested Idea 19: JavaScript JSON convertors for graph file formats, but I
would like to drop the word “graph” from it, because this project will support
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>,
Xlsx).</p>
<p class=MsoNormal>Xgmml, Graphml, Sif, Nnf, Gml (,Csv, 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
class=GramE>) .</span></p>
the project is finished well before the deadline (see the timeline for details)
.</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"
alt="Description: Description: C:\Users\Abhas_2\Desktop\cyto\cyto_proposal.png"
src="cyto_proposal_draft_files/image001.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>
and <span class=SpellE>jquery</span> will be used for parsing the xgmml file.
Then some JavaScript code (using looping and if needed, regular expressions)
will deal with the parsed xml file to convert them correctly into <span
class=SpellE>javascript</span> variables and objects. Finally, they can be used
to generate its json representation. (Maybe, take some inspiration from this
library in Gremlin (written in java): <a
will be dealt with first. Xml parsers available in native javascript and jquery
will be used for parsing the xgmml file. Then some JavaScript code (using
looping and if needed, regular expressions) will deal with the parsed xml file
to convert them correctly into javascript variables and objects. Finally, they
can be used 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>
)</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>
“edge” is represented by “group” in json. All its data is stored in the “data”
object.</p>
</span></span></span><![endif]>Whether it is a “node” or a “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:
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
class=SpellE>nodeTransparency</span>&quot; value=&quot;1.0&quot;/&gt;<o:p></o:p></span></p>
style='mso-spacerun:yes'>            </span>&lt;att
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
class=SpellE>nodeLabelFont</span>&quot; value=&quot;Default-0-12&quot;/&gt;<o:p></o:p></span></p>
style='mso-spacerun:yes'>            </span>&lt;att
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
part&quot;],<o:p></o:p></span></p>
Component&quot;:[&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
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
class=GramE>fill</span>&quot;:&quot;#<span class=SpellE>fcfffd</span>&quot;,<o:p></o:p></span></p>
style='mso-spacerun:yes'>                           
</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
class=SpellE><span class=GramE>cytoscapeNodeGraphicsAttributes</span></span>&quot;:{<o:p></o:p></span></p>
style='mso-spacerun:yes'>   </span><span
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>}<o:p></o:p></span></p>
style='mso-spacerun:yes'>          </span><span
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;:
&quot;nodes&quot;<o:p></o:p></span></p>
style='mso-spacerun:yes'>      </span>&quot;group&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
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
implementation process is same as that of the previous one. Only the code will
be different to take care of the syntax difference of these formats.</p>
</span>Graphml is also a xml-based format, so the implementation process is
same as that of the previous one. Only the code will be different to take care
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
class=GramE>( </span><a
</span></span></span><![endif]>Make use of the graphml – attribute values ( <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
graphml – attribute values )</p>
data of type “attr.type” (which are provided as 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"
alt="Description: Description: C:\Users\Abhas_2\Desktop\cyto\cyto_implementation.png"
src="cyto_proposal_draft_files/image002.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
written to take care of these file formats. There is already a python-based
</span></span></span><![endif]>Sif and Nnf: Very simple jS code needs to be written
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
class=SpellE>js</span> or possibly using xregexp library <a
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
custom-made parser needs to be built based on regular expressions (native js or
possibly using xregexp library <a href="http://xregexp.com/">http://xregexp.com/</a>
). The rest of the plan is the same as that of xgmml, 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
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"'>node<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>0<o:p></o:p></span></p>
style='mso-tab-count:1'>            </span>id<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
style='mso-tab-count:1'>            </span><span class=GramE>label</span><span
style='mso-tab-count:1'>     </span>&quot;YKR026C&quot;<o:p></o:p></span></p>
style='mso-tab-count:1'>            </span>label<span 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
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:1'>          </span>1916.0<o:p></o:p></span></p>
style='mso-tab-count:2'>                        </span>x<span 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
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
class=SpellE><span class=GramE>type</span>&quot;:&quot;ellipse</span>&quot;,<o:p></o:p></span></p>
style='mso-spacerun:yes'>                            </span>&quot;type&quot;:&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-spacerun:yes'>                            </span>&quot;<span
class=GramE>fill</span>&quot;:&quot;#E1E1E1&quot;,<o:p></o:p></span></p>
style='mso-spacerun:yes'>                           
</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;:
&quot;nodes&quot;<o:p></o:p></span></p>
style='mso-spacerun:yes'>      </span>&quot;group&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
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
after the completion of the whole project, so there is no way that they will
harm the main project. I am aware that new GSOC applicants like me tend to
propose a lot more than they can actually complete, so I have tried not to fall
in that trap. But these extras are here, because I plan to do them in the
future, within or after GSOC.<span style='mso-spacerun:yes'>  </span>Also, as a
side note, in future, I wish to release this codes as a separate jS library for
converting customized-xml formats into json (I hope my mentoring org will allow
this).</p>
<p class=MsoNormal>These extras will be done only if there is ample time left after
the completion of the whole project, so there is no way that they will harm the
main project. I am aware that new GSOC applicants like me tend to propose a lot
more than they can actually complete, so I have tried not to fall in that trap.
But these extras are here, because I plan to do them in the future, within or
after GSOC.<span style='mso-spacerun:yes'>  </span>Also, as a side note, in
future, I wish to release this codes as a separate jS library for 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
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
part. I wouldn’t have tried this if there was no cross-browser external library
to read and write xlsx format. But thankfully and quite surprisingly, there is
one called Xlsx.js <a href="https://github.com/stephen-hardy/xlsx.js">https://github.com/stephen-hardy/xlsx.js</a>
style='color:red'> </span>This is the most challenging part. I wouldn’t have
tried this if there was no cross-browser external library to read and write
xlsx format. But thankfully and quite surprisingly, there is 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
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
community and they will be given more importance than the extras)</p>
<p class=MsoNormal>(Feedback will be obtained for all the converters from the community
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 checker might not be possible in case of non-xml based formats. )</p>
a xml-checker and discard non well-formed files. Such a checker might not be
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
wish to linger with the Cytoscape.js project.</p>
Cytoscape project but as I am not a Java developer, I wish to linger with the
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>
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<o:File HRef="image001.png"/>
<o:File HRef="image002.png"/>
<o:File HRef="image003.png"/>
<o:File HRef="filelist.xml"/>
</xml>
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