Cytoscape User Group, Toronto (CyT.O.)

Goal: Help users learn to use Cytoscape to answer biologically relevant questions by providing information, tutorials and linking new with experienced users.

Meeting 1 – Introduction and organization

• [attachment:2008Feb4_CyTO-mtg1.ppt Gary's presentation is now online]

• Date & Location: [http://tdccbr.med.utoronto.ca/Home.aspx?event_id=8281&PageID=111&view=event_view Mon.Feb.4 at 3pm, CCBR Red Room]

• Cytoscape introduction presentation and demo (Gary Bader) - Overview of biological network analysis questions that can be answered using Cytoscape
• Introduce knowledgeable Cytoscape users
• Discuss organization of regular Cytoscape user group meetings

  • Central meeting organization page on Cytoscape wiki “TorontoUserGroup”

  • Sign up to Google Group mailing list – cytoscape-toronto@googlegroups.com – have an email sign up sheet at the meeting to get this list started

    • Group homepage: http://groups.google.com/group/cytoscape-toronto?hl=en

  • Develop list of experienced Cytoscape users in Toronto
  • Decide
    • Meeting frequency? Monthly or every 2 months?
    • Duration? 1 hour?
    • Location: CCBR Red Room
  • Ask participants for suggestions for things to discuss at normal meetings
• Help us advertise - please forward this information to a friend.

Subject: Cytoscape User Mtg. - Mon.Feb.4 @3pm, CCBR Red

Are you interested in network and pathway analysis of biological data?

Cytoscape (www.cytoscape.org) is free network visualization and analysis software, partly developed at UofT!

You can use Cytoscape to:
-Visualize networks and associated cellular data and create publication quality network diagrams
-Analyze biological interaction networks and pathways
-Analyze gene and protein expression data
-Perform text mining of molecular interactions from PubMed Abstracts
-Download biological networks from multiple databases
-Develop your own network analysis software

Please join us for an initial meeting of the Toronto Cytoscape user group, held to help users learn to use Cytoscape to answer biologically relevant questions by providing information, tutorials and linking new with experienced users.

Monday Feb.4.2008 in the CCBR Red Room from 3-4pm.

Gary Bader (www.baderlab.org) will provide a Cytoscape overview and together we will plan future meetings. Knowledgeable Cytoscape users will be on hand to meet with and answer your questions.

More details at:
http://www.cytoscape.org/cgi-bin/moin.cgi/TorontoUserGroup

Normal meetings

• Tutorial/discussion about specific Cytoscape topic. Topics selected from a list, by demand/request from participants
• Potential tutorial topics

  • Review [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17947979 Nature Protocols] paper about Cytoscape

  • Specific plugins e.g. BiNGO, MCODE, ActiveModules

  • Developer plugin writing tutorial
  • How to test Cytoscape and provide feedback to the core developers to make Cytoscape better.
• User demo sessions: what cool ways have you used Cytoscape?
• User experience and feedback sessions
• Cytoscape news – status of latest Cytoscape development, new papers using Cytoscape, developer participants, recently released plugins

Documents

• Cytoscape poster announcing the first meeting designed by Vuk Pavlovic

attachment:CytoscapePoster.png