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/)
  • 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@…)
    • 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
  • visualize a whole genome data from chromosome level to sequence level seamlessly and interactively
  • easy to use user interface and provide some new accessibility features
  • genome oriented DAS client
  • built in C++, OpenGL.

• 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