Cytoscape retreat 2010 day 1

2010-07-28T18:24:00.031+09:00

I attended this year's Cytoscape retreat in University of Michigan. I think it was quite good. I wrap up the Day 1.

First, a bit about the meeting. This is a meeting of Cytoscape plugin developer, user, and the principal investigators in each research institute (UCSD, University of Toronto, UCSF, NCIBI).

Day 1 covered a bit of introduction(tutorials for user and plugin developer) and then a diversity of plugin developer talks. All of them were interesting. I also talked about my plugin, here I summarize the talks except mine.

Analyzing biological networks with CentiScaPe

This plugin calculates various centralities with graphical plot.

This centrality calculation is commonly-performed for understanding biological network topology.

Web service client and server for phosphositeplus database

Sasha Tkachev (bioinformatics software programmer from Cell Signaling Technology) introduced the client plugin for PhosphoSitePlus.

PhosphoSitePlus is a database manually curated phosphorylation site database.

You can download the plugin from here.

I asked Sasha after his talk, "Any document about phosphositeplus client plugin?". He said "No".

He also said "There might be some problems, If you find, please report me."

CID

CID stands for Cross-species Interactome Database.

This seems to enabled researcher to infer the pathway about aging.

The functions seems to inferring pathway from orthoMCL and GO information.

Please see reference

Metscape

This is a client plugin for NCIBI database collected human compound information from HUMDB, EHMN, and KEGG.

This plugin generates a metabolic reaction network from compound names related the reactions.

PanGIA

A plugin by Gregory Hannum (UCSD Ideker lab)

For more detail, please see his and his colleague's paper.

Ortho-nets

This plugin generates domain co-occurrence networks in multiple organisms using information in iRefindex.

http://wodaklab.org/orthonets/

OndexView

This plugin generates relational network using triples from several major biological databases.

In short, triple is a relation made from "Subject", "Predicate", and "Object", like "A enzyme(Subject)", "catalyzes(Predicate)", "A reaction(Object)".

http://www.ondex.org/

Genemania

This is Cytoscape plugin version of Genemania by Bader lab.

http://www.genemania.org/search.jsf

http://www.genemania.org/plugin

Genemania is a gene prediction software. Jason Montojo talked about the plugin version of Genemania.

http://genomebiology.com/2008/9/S1/S4

Enrichment Map

A geneset enrichment analysis plugin as its name suggests.

Please see reference

MiMI plugin

A client plugin for NCIBI database MiMI