Satellite meeting for Data Visualization

Topics

Visualization for large datasets including:

• Protein-Protein Interaction
• Pathways
• Genome
• other

This includes development of easy-to-use backend data services such as

• Interaction network data service
• Annotation service

Chairperson

• .

Participants

• Bruno Aranda (baranda@…)
• Keichiro Ono (kono@…)
• Soichi Ogishima (ogishima@…)
• Kozo Nishida (kozo-ni@…)
• Yasukazu "yaskaz" Nakamura (yaskaz at ddbj.org)
• Shinobu Okamoto ( so at kazusa.or.jp -- GenoDive)
• Kunihiro Nishimura (kuni at cyber.t.u-tokyo.ac.jp -- GenoDive)
• Add yourself! :)

Targets

• Last yeat in the hackathon, we have developed a common query web service API for interaction databases called PSICQUIC. Some of the service providers have published their service and now we should think about how to use the service in client and make them easy-to-use for all service users.
• The goal of this group is the following:
  • Make backend service more easy-to-use client software
    • Cleaner API
    • REST support
  • Create intuitive UI for client software
  • Design more sphisticated visualization

Date

• Most of the time during the hackathon. Feel free to join anytime :-)

Room

• Chura Hall (3F)

Presentations

Fill:

• Name of the presenter
  • Title of the talk
  • Attachments (PPT or PDF slides etc.)

Notes

• BioMartApiRequest

• Software
  • Cytoscape
  • GraphViz?
  • Ubigraph
  • E-cell 3D
  • N-Browse
  • BioCichlid?
  • GenoDive?

• Data Provider
  • Interactions
    • IntAct?
    • MINT
    • BioGRID
    • STRING
  • Pathways
    • KEGG
    • Reactome
    • BRENDA
  • Annotations(service)
    • Biomart
    • Entrez Gene

• Large-Scale Data Visualization
  • Backend
    • Import data - PSICQUIC, DAS-MI
    • Edit data in database interactively - how?

• Interactivity

• VisualizationWg

Results

• Generic ID mapping for GenMAPP Data Import plugin ( by Isaac Ho / UCSF )

GenMAPP-CS is a next-generation implementation of GenMAPP, a metabolic pathway visualization tool, as a set of plugins for Cytoscape. This week I worked on creating a way to map the ids of any network based on GenMAPP-supported data libraries ( e.g, KEGG, Affy, Ensembl ) to the ids of any expression data based on these libraries. The solution involves converting all ids to Ensembl IDs upon import, and calling a webservice on GenMAPP's services which are tied to their MySQL dbs. Kei Ono and I collaborated briefly in discussing the best place in the plugin code to place the responsibility for id conversion.

• How to create Processing OSGi bundle (Japanese)
  •  http://d.hatena.ne.jp/kozo-ni/20090318#1237335991
• pARP 3D visualization prototype (by Jan@Sanger, Kunihiro@UT)
  • Got detail display working (on right hand side):  http://www.flickr.com/photos/82932180@N00/3364927005/
  • Kunihiro wrote a proof-of-concept for 3D (to display multiple individuals simultaneously) in processing:  http://www.flickr.com/photos/82932180@N00/3368845815/

TODOs

• Visualize time-series microarray data using Cytoscape
  • Animation (using dynamic layout)
• More biologically meaningful graph layout
  • List up several methods of graph layout