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<h1> </h1>
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<div style='border:none;border-bottom:solid #4F81BD 1.0pt;padding:0in 0in 4.0pt 0in'>
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<p class=MsoTitle>JavaScript JSON convertors for Cytoscape 3.0 file formats</p>
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</div>
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<p class=MsoNormal> </p>
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<h1>Project Idea:</h1>
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<p class=MsoNormal> </p>
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<p class=MsoNormal>The project title is: JavaScript JSON convertors for
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Cytoscape 3.0 file formats.</p>
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<p class=MsoNormal> The idea is based upon suggested Idea 19: JavaScript JSON
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convertors for graph file formats, but I would like to drop the word “graph”
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from it, because this project will support virtually all formats accepted by
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Cytoscape 3.0 .</p>
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<h1>Synopsis:</h1>
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||||
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<p class=MsoNormal> </p>
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||||
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<p class=MsoNormal>This project deals with the conversion of different graph
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||||
and other formats used in Cytoscape 3.0 to Json used in cytoscape.js and vice
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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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representations of the data. It is not an easy task to create json
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representation of a required graph by hand. This is where this project comes
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in. I will develop some converters using JavaScript which will automate this generation
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of json representation. Cytoscape-web, the predecessor of Cytoscape.js
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supported only sif files, but this project will support import and export to
|
||||
all the formats mentioned earlier.</p>
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<h1>Implementation details:</h1>
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||||
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<p class=MsoNormal> </p>
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||||
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<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>
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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
|
||||
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)
|
||||
.</p>
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||||
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<p class=MsoNormal><img width=624 height=416 id="Picture 2"
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||||
src="cyto_proposal_draft_files/image001.png"
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||||
alt="Description: C:\Users\Abhas_2\Desktop\cyto\cyto_proposal.png"></p>
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||||
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<p class=MsoNormal>Now, this is how I plan to deal with each of them.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-.25in'>1.<span style='font:7.0pt "Times New Roman"'>
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||||
</span>Xgmml: This is the top priority format and hence will be dealt with
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||||
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>
|
||||
|
||||
<p class=MsoNormal style='margin-left:.5in'>This required some separate
|
||||
functions which can:</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;text-indent:-.25in'><span
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||||
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>convert parsed xml to jS variables and objects</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;text-indent:-.25in'><span
|
||||
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>create xml from given jS variables and objects</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;text-indent:-.25in'><span
|
||||
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>save given jS variables and objects as json</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;text-indent:-.25in'><span
|
||||
style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>convert json into given jS variables and objects</p>
|
||||
|
||||
<p class=MsoNormal style='margin-left:.5in'> </p>
|
||||
|
||||
<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in'>2.<span
|
||||
style='font:7.0pt "Times New Roman"'> </span>Graphml:
|
||||
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=MsoListParagraphCxSpMiddle> </p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle>Before I move on to the other ones, here
|
||||
is a small chart for reference:</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpLast> </p>
|
||||
|
||||
<p class=MsoNormal><img border=0 width=623 height=363 id="Picture 1"
|
||||
src="cyto_proposal_draft_files/image002.jpg"
|
||||
alt="Description: C:\Users\Abhas_2\Desktop\cyto\cyto_implementation.png"></p>
|
||||
|
||||
<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in'>3.<span
|
||||
style='font:7.0pt "Times New Roman"'> </span>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> . Nnf files will be stripped off its network information and treated just
|
||||
like a Sif file (Possible problem with multi-network files ??)</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpLast style='text-indent:-.25in'>4.<span
|
||||
style='font:7.0pt "Times New Roman"'> </span>GML:
|
||||
A 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.</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 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. 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'>5.<span
|
||||
style='font:7.0pt "Times New Roman"'> </span>Csv:
|
||||
Use any well-documented csv parser and rest is the same.</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpLast style='text-indent:-.25in'>6.<span
|
||||
style='font:7.0pt "Times New Roman"'> </span>Xlsx:
|
||||
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 .xlsx .</p>
|
||||
|
||||
<p class=MsoNormal> </p>
|
||||
|
||||
<h1>Timeline:</h1>
|
||||
|
||||
<p class=MsoNormal> </p>
|
||||
|
||||
<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%'>1.<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>Before June 17 : </p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%;font-family:"Courier New"'>o<span
|
||||
style='font:7.0pt "Times New Roman"'> </span></span>Learn
|
||||
more about:</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%;font-family:"Courier New"'>o<span
|
||||
style='font:7.0pt "Times New Roman"'> </span></span> Jquery,
|
||||
xregexp, csv-parser, json, xlsx.js and the graph formats.</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%;font-family:"Courier New"'>o<span
|
||||
style='font:7.0pt "Times New Roman"'> </span></span>Set up
|
||||
development environment</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%'>2.<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>June 17 – July 6 (18 days): Implement xgmml converter</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%;font-family:"Courier New"'>o<span
|
||||
style='font:7.0pt "Times New Roman"'> </span></span>June 17 –
|
||||
June 29 (12 days): Implement xgmml parser</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%;font-family:"Courier New"'>o<span
|
||||
style='font:7.0pt "Times New Roman"'> </span></span>July 30 –
|
||||
July 5 (6 days): Rest of the converter</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%'>3.<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>July 5 – July 7 (3 days): Test converter with different xgmml
|
||||
files.</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%'>4.<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>July 8 – July 25 (18 days): Implement graphml converter</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%;font-family:"Courier New"'>o<span
|
||||
style='font:7.0pt "Times New Roman"'> </span></span> July 8 –
|
||||
July 19 (12 days): Implement graphml parser</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%;font-family:"Courier New"'>o<span
|
||||
style='font:7.0pt "Times New Roman"'> </span></span>July 20 –
|
||||
July 25 (6 days): Rest of the converter</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%'>5.<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span> July 26 – July 28 (3 days): Test graphml converter</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%'>6.<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>July 29 (Mid-term evaluation): Deliver fully-implemented xgmml
|
||||
and graphml parser.</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%'>7.<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>July 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>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%'>8.<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>July 31 – August 2 (3 days): Implement and test Sif and Nnf
|
||||
converter.</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%'>9.<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>August 3 – August 20 (18 days): Implement Gml converter (First 12
|
||||
days for the parser).</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%'>10.<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>August 21 – August 23 (3 days): Test Gml converter</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%'>11.<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>August 24 – August 27 (4 days): Put all the converters together
|
||||
and test them (Packaging).</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%'>12.<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>August 28 – September 3 (10 days): Prepare documentation and add
|
||||
inline comments in the code.</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpLast style='text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%'>13.<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>September 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 of more importance than the extras)</p>
|
||||
|
||||
<h1>Possible hurdles:</h1>
|
||||
|
||||
<p class=MsoNormal> </p>
|
||||
|
||||
<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%'>1.<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>Json handler in Cytoscape.js might not be able to handle objects
|
||||
within the “data” section. If so, request the developer or send a patch to the
|
||||
core project so that it is supported.</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%'>2.<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>Make sure the regular-expression based Gml parser is not buggy.</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpLast style='text-indent:-.25in'><span
|
||||
style='font-size:10.0pt;line-height:115%'>3.<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>The 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 possible in case of non-xml based formats. )</p>
|
||||
|
||||
<h1>What can I bring to the team?</h1>
|
||||
|
||||
<p class=MsoNormal> </p>
|
||||
|
||||
<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in'><span
|
||||
style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>Yes, I am committed in working hard for this GSOC project this
|
||||
summer. I do not have any other commitment during the summer other than my
|
||||
college internals for the next session which should be held near the end of
|
||||
August or the start of September. I am not yet sure about the date, but I will
|
||||
ask for a one-week break during that time. I hope it won’t be much of a
|
||||
problem.</p>
|
||||
|
||||
<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in'><span
|
||||
style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>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'><span
|
||||
style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'>
|
||||
</span></span>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>
|
||||
|
||||
</div>
|
||||
|
||||
</body>
|
||||
|
||||
</html>
|
||||
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Reference in New Issue
Block a user