Need Good Cytoscape Tutorial

Question

[williamjohn360]

Hello,

I am new to network analysis. I willing to use cytoscape for my work. Although cytoscape has tutorial, is there any advanced level tutorial to learn (with worked out example)?

Answer 1

[jackuser1979]

Cytoscape has excellent manual with examples http://home.cc.umanitoba.ca/~psgendb/birchhomedir/BIRCHDEV/doc/cytoscape/manual.pdf

For further reading:

1. Kohl et al. (2011) Cytoscape: software for visualization and analysis of biological networks. Methods Mol Biol 696:291-303.(pmid: 21063955)
2. Shannon et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498-504. (pmid: 14597658)
3. Cline et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2:2366-82. (pmid: 17947979)
4. Killcoyne et al. (2009) Cytoscape: a community-based framework for network modeling. Methods Mol Biol 563:219-39. (pmid: 19597788)
5. Smoot et al. (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27:431-2. (pmid: 21149340)
6. Merico et al. (2011) Visualizing gene-set enrichment results using the Cytoscape plug-in enrichment map. Methods Mol Biol 781:257-77.(pmid: 21877285)

[Diwan]

I particularly found this paper very helpful:"Cline et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2:2366-82. (pmid: 17947979)"

Answer 2

[Giovanni M Dall'Olio]

The best thing is to ask to the Cytoscape Mailing list. Moreover, there are many workshop about Cytoscape; you may find materials about them in slideshare and in google.