Day 3: Visualization Workgroup Discussion

Hands on: March 19 AM at the seminar room

Tools

• Network
  • Cytoscape was presented by Keiichiro@UCSD
  • 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
  • google GenomeBrowser
  • eeDB

Usecase/Data

• Cytoscape
  • retrieve a organism's all metabolic reactions from KEGG