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Day 3: Visualization Workgroup Discussion
Hands on: March 19 AM at the seminar room
Tools
- Network
- Cytoscape was presented by Keiichiro@UCSD ( http://www.cytoscape.org/index.php )
- E-Cell 3D was presented by Kazuharu@Keio ( http://ecell3d.iab.keio.ac.jp/ )
- GraphViz
- BioCichlid by Soichi@tmd -- http://newton.tmd.ac.jp/
- EdgeExpressDB (eeDB) was presented by Jessica@RIKEN ( http://fantom.gsc.riken.jp/4/ -- currently protected; available soon)
- Expression
- Cytoscape
- Genespring
- TMeV
- PREP+07
- bluejay
- Biocichlid
- eeDB
- GenoDive (maybe ..)
- Genome
- Ensembl
- UCSC
- GBrowse
- PARP (multi genomes: m) waspresented by Jan@Sanger
- GenoDive was presented by Shinobu@Kazusa and Kunihiro@UT ( http://genodive.org/ -- download page is in prep)
- CGAS (m) by Masumi@hokudai ( http://cgas.ist.hokudai.ac.jp )
- Genome Projector was presented by Kazuharu@Keio ( http://www.g-language.org/g3 )
- bluejay
- X..map ( http://xmap.picr.man.ac.uk/ )
- google GenomeBrowser
- eeDB
Usecase/Data
- Cytoscape
- retrieve a organism's all metabolic reactions from KEGG
- convert node format from [compound -> enzyme -> compound] to [compound -> compound] or [enzyme -> enzyme] like following paper
