CIShell Manual : Hackathon Result

Case study was the Existing web semantic Gephi web semantic Gephi plugin plugin as a reference to Nick's work : http://wiki.gephi.org/index.php/SemanticWebImport

source code : https://gforge.inria.fr/scm/?group_id=3504

GEPHI plugin references :

https://wiki.gephi.org/index.php/Plugins_portal

https://gephi.org/developers/

There are two levels of CISHELL interoperability to achieve such a thing :

1- the GEPHI toolkit which provides the trunk GEPHI API

2- the specific GEPHI plugin level

1- A GEPHI TOOLKIT cishell port :

GEPHI is available as a GEPHI TOOLKIT JAR.

see : https://gephi.org/toolkit/

The very first CiSHELL pulgin implementation we could imagine is a translation APIs layer wihch interface the GEPHI TOOLKIT specific API and data structures to the CiSHELL one.

If GEPHI TOOLKIT were a OSGI, it'd be easier but we'd still need this glue CiSHELL plugin to interface it I guess.

This implementation should map data structures and methods :

In GEPHI we would need to get into Graph API (https://wiki.gephi.org/index.php?title=Graph_API) and the Attribute API (https://wiki.gephi.org/index.php?title=Attributes_API) to feed CISHELL context with the mandatory format described (here ?)

2- Gephi plugin - CiSHELL plugin

The bundle plugin distribution format in GEPHI is NBM (NetBeans Module, a software component for the NetBeans platform).

It's binary and highly compressed.

But there ise a NBM file to JAR utility : http://gephi.org/pipermail/gephi-plugins/2011-February/000055.html

Then a simple CiSHELL plugin could port the GEPHI plugin by using its JAR a dependency to GEPHI TOOLKIT CiSHELL port to benfecit from memory translation done on GEPHI generic level.

3- both ways interoperability and possible other player like cytoscape

The architecture and management of such a project should target a both ways interoperability for both environnement GEPHI and CISHELL to benefit one from an other.

Also the meta architecture design should target to prepare future exchange with other environnement like cytoscape.

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CIshell-GeneMANIA git repo:

git@github.com:jrrmzz/cishell-genemania.git

http://www.genemania.org/

Thanks again for a great workshop! As promised, here's the GeneMANIA source code. The Lucene bits are in common/src/main/java/org/genemania/mediator/lucene. You'd probably want to have a look at LuceneMediator, which has most of the mapping code. It uses cglib's Enhancer class to defer the construction of the object graph until the appropriate getters are called.

https://dl.dropbox.com/u/17376778/genemania_snapshot_20121119.zip

If you want our data in plain text format, we have it hosted here: http://pages.genemania.org/data/

Please let me know if you have any questions. If you want to compile and run this, the provided READMEs give details about how to get started.

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Experimental Rappture-to-CIShell converter script:

https://nanohub.org/infrastructure/rappture/wiki/CIShell

--Michael McLennan, Purdue University