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About this document

This is an official Request for Comment (RFC) for training new users.

For details on RFCs in general, check out the Wikipedia Entry: Request for Comments (RFCs)

Status

May 18, 2007 - RFC creation. Open for public comment

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Proposal

As Cytoscape undergoes continuous improvement, there is a constant need for revisions to the tutorials. In addition to making the most current content available, we are aiming to provide users with comprehensive and quality training resources. This will make the software more accessible to new users and introduce advanced users to powerful functionality that they can efficiently implement.

Ideally, we would like to compile a “toolbox” of educational resources and develop a strategy for effectively training Cytoscape users.

Possible tools include:

• “Canned” tutorials – prefabricated resources allowing users to teach themselves. This is what we are currently using, with tutorials found on the Cytoscape website and scattered throughout the user manual.
• Mailing list – also in use (cytoscape-discuss). This is not explicitly a teaching tool, but is often used as one. The archives serve as a user-directed FAQ section.
• Live demos – onsite training given by Cytoscape staff.
• Conference tutorials – presentations given at various conferences. (See General Notes)
• Others?

Biological Questions / Use Cases

• How do I start using Cytoscape?
• How do I perform basic/common/necessary tasks?
• How do I perform advanced/specialized tasks?
• Using plugins (each one is responsible for its own tutorials)

The current tutorials already address these general use cases by being structured around completing a task, instead of comprising a feature list of technical specifications. They are by no means exhaustive, but do aim to integrate different functions of Cytoscape into a coherent whole by modeling a possible project. Perhaps we can extend this task-oriented strategy to other resources as well.

General Notes

Some suggested conferences:

1. ISMB: Intelligent Systems for Molecular Biology (http://www.iscb.org/ismbeccb2007/registration/)

   • Opportunities offered: tutorials (4 h), proposal template exists on site
   • 2007 conference July 21-25; proposal deadline was Dec. 15
   • 2008 conference date unknown

2. AAAS: American Association for the Advancement of Science (http://www.aaas.org)

   • Opportunities offered: special sessions (3 h) with multiple sessions possible
   • 2008 conference Feb. 14-18

3. ICSB: International Conference on Systems Biology (http://www.icsb-2008.org)

   • Opportunities offered: tutorials (3 h) before the conference
   • 2007 conference Oct. 1-6; deadline was Apr. 30
   • 2008 conference tutorial presentations Aug. 22 – 23; submit 1 page pdf

4. PSB: Pacific Symposium on Biocomputing (http://psb.stanford.edu/cfp.html)

   • Opportunities offered: in-depth (3 h) or survey (1 h) tutorials
   • 2008 conference Jan 4-8
     • submit paper (12 pg max) by July 16, camera-ready tutorial handouts by Nov. 5

     • example tutorial proposals at http://psb.stanford.edu/psb01/tutorial-hiperf.html and http://psb.stanford.edu/psb01/tutorial-network.html and http://mgl.scripps.edu/people/sanner/html/talks/PSB2001talk.html

5. RECOMB: Research in Computational Molecular Biology (http://www.comp.nus.edu.sg/~recomb08/)

   • Opportunities offered: papers (25 min oral), posters, satellite workshops
   • 2008 conference Mar. 30 – Apr. 2; submit papers by Sept. 24 and posters by Feb. 4

6. ASMS: American Society for Mass Spectrometry (http://www.asms.org)

   • Opportunities offered: tutorials (1.5 h), short courses (1 or 2 full days)
   • 2007 conference June 3-7; abstract deadline was Feb. 2
   • 2008 conference June 1-5; abstract deadline unknown

7. FASEB: Federation of American Societies for Experimental Biology (http://faseb.org)

   • Organizes multiple Summer Research Conferences each year, and member organizations hold independent conferences as well
   • example: Experimental Biology, Apr 5-9, 2008
   • example: American Society of Human Genetics, Oct 24-26, 2008: 1.5-2 h sessions

8. FOCIS: Federation of Clinical Immunology Societies (http://www.focisnet.org/index.php)

   • a federation structure of 20 Member Societies and 15 Affiliate Societies, working in areas such as Rheumatology, Dermatology, Diabetes, Cytokine Research, Blood and Marrow Transplantation.
   • 2007 conference June 7-11, San Diego
   • 2008 conference June 5-9, Boston
   • 2009 conference June 11-15, San Francisco

9. AIChE: American Institute of Chemical Engineers (http://www.aiche.org/)

   • perhaps somewhat of a departure from the biological audience but their annual meetings are huge affairs which in the past have include Systems Biology tracks.
   • 2007 annual meeting November 7-9, Salt Lake City

10. AACR: American Association for Cancer Research (http://www.aacr.org/)

    • oldest and largest scientific association focused on cancer research.
    • has a variety of educational programs and conference programs
    • 2008 annual meeting April 12-16, San Diego

    • conference on Approaches to Complex Pathways in Molecular Epidemiology, May 30 - June 2, Albuquerqe (http://www.aacr.org/home/scientists/meetings--workshops/special-conferences/approaches-to-complex-pathways-in-molecular-epidemiology.aspx)

    • many other conferences listed at (http://www.aacr.org/home/scientists/meetings--workshops/meetings--workshops-calendar.aspx)

11. American College of Cardiology (http://www.acc.org/index.htm)

    • holds many conferences and education programs, one of the largest being the Innovations in Intervention Summit (I2)
    • Research that used Cytoscape (at Stanford Medical School and Agilent) was presented at annual scientific session in 2006.
    • 2008 annual conference, March 29 - April 1, Chicago

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