== 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
  * 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
     * http://bioinformatics.oxfordjournals.org/cgi/content/full/22/14/1767