== 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 * Cytoscape
   * kozo-ni's usecase
     * 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
     * calculate betweeneth and find bottlenecks (currently I use CentiScaPe plugin or igraph[R library])
     * map gene expression to enzyme
  * Genespring
  * TMeV
  * PREP+07
  * bluejay
  * Biocichlid
  * eeDB
  * !GenoDive
     * will be available with GFF3 file or from DAS server

 * Genome
  * Ensembl
  * UCSC
  * GBrowse
  * PARP (multi genomes: m) waspresented by Jan@Sanger  (http://github.com/jandot/parp/tree/double_circular)
  * !GenoDive was presented by Shinobu@Kazusa and Kunihiro@UT ( http://genodive.org/ -- download page is ''in prep'')
  * A genome viewer projected on a wall type display was presented by Kunihiro@UT
  * CGAS (m) by Masumi@hokudai ( http://cgas.ist.hokudai.ac.jp )
  * Genome Projector was presented by Kazuharu@Keio ( http://www.g-language.org/GenomeProjector/ )
  * bluejay  ( http://bluejay.ucalgary.ca/ )
  * X..map  ( http://xmap.picr.man.ac.uk/ )
  * google !GenomeBrowser
  * eeDB
  * MaDaS ( http://madas2.bioinfo.cnio.es/ , click on "Go directly to example" in order to see an example)

== Usecase/Data ==
 * Cytoscape
   * kozo-ni(kozo-ni@is.naist.jp)
     * usecase
       * retrieve an 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
       * calculate betweeneth and find bottlenecks (currently I use CentiScaPe plugin or igraph[R library])
       * map gene expression to enzyme
     * data
       * affymetrix gene-chip expression data
     * functionality needs
       * get an organism's all metabolic reactions from KEGG
       * draw enzyme or compound centric network. (In enzyme centric network, enzyme nodes share a common compound. In compound centric network, compound nodes share a common enzyme.)
       * time-series expression mapping function
     * difficulty
       * blah,blah,blah 

 * E-Cell 3D
  * show dynamics of cellular simulations as well as the network
  * debug a simulation model - a molecule could be depleted or too concentrated, steady-state (balanced flux), rhythms
  * looking at the overall behavior

 * Genome Projector
  * look at a feature of interest from several different perspectives (zoom level + context)
  * overlay data

 * pARP
  * show links between several features on one genome, e.g. mappings of readpair data

 * !GenoDive
  * data
      * from DAS server

 * CGAS
  * visualize sequence alignments of genome sequences by dot plot with annotations.
  * dynamic zooming and browsing.
  * data
    * users' alignment data & annotation from NCBI.

== Future directions ==
 * semantic zooming
  * need for queries (DAS?) to define semantic abstraction of data
  * server-side implementation to handle semantic abstraction level of returned data