Version 60 (modified by severin, 15 years ago)

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Day 3: Visualization Workgroup Discussion

Hands on: March 19 AM at the seminar room

Tools

  • Expression
    • Cytoscape * Cytoscape
    • Genespring
    • TMeV
    • PREP+07
    • bluejay
    • Biocichlid
    • FANTOM4 eeDB - Jessica Severin@RIKEN
    • genoDive
      • will be available with GFF3 file or from DAS server

Usecase/Data

  • Cytoscape
    • kozo-ni(kozo-ni@…)
      • usecase
      • 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