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.
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)
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
http://mimi.ncibi.org/MimiWeb/main-page.jsp
GLay GSearcher
Layouting and searching plugins by Gang Su.
So the names are (G)Lay[out] and (G)Searcher.
He also talked at last Cytoscape retreat 2008 as a Google summer of code project student.
This new GLay can utilize igraph layout algorithms by using C++ and JNI (However compatible with only Windows).
GSearcher enables to regular expression search to multiple attribute.
You can see these talk videos from NCIBI.
http://portal.ncibi.org/gateway/cytoscape2010.html
