Cytoscape book discussion

Date: Friday, July 18, 2008


Should we publish a co-authored book on Cytoscape and its role in exploring biological networks as a companion to 3.0 release?

We have been approached frequently to write book chapters on Cytoscape. But there is so much functionality to write about that it is hard to capture in a book chapter. At the same time, there appears to be a niche for a practitioner-oriented book on biological networks and their analysis, visualization, and integration with measurement data. A book on Cytoscape, co-authored and published in the time frame to be a companion to the 3.0 release, would serve a number of purposes:

  1. a comprehensive and useful resource for the community of Cytoscape users and developers.
  2. a comprehensive and useful resource for anyone who wanted to learn more about biological network analysis and visualization.
  3. a way of broadening the user and developer base for Cytoscape.
  4. a way to enhance Cytoscape's stature and visability.

We are currently thinking of this book as consisting of set of case study chapters, each one written from a scientist end-user point of view about the use of Cytoscape in solving a biology (or non-biological) problem. The case study would describe the problem in some depth, describe why Cytoscape was chosen (perhaps why other tools/types of tools were not), what features of Cytoscape were used & how to reach the end point—all from the user’s point of view. In sidebars, we could present developer commentary in some form that helps (core, plugin) developers understand how to develop Cytoscape for end-users.

This discussion will go over the benefits/costs/risks of doing this work and help us decide whether to move forward. Also, if we decide to move forward, then we want to identify people who will volunteer to write chapters and/or to serve as editors.



Book discussion

  1. Concern: it will get out of date. But we can focus on concepts that don’t change.
  2. There are some biological network books that exist (Allan has a couple), but they seem to be very mathematical.
  3. Is this useful for someone on the tenure track? Not really. Almost no credit for writing books, especially for NIH funding. Instead, publishing in peer-reviewed journals is required.
  4. Concern: book isn’t the right format, since typical references are online. Maybe we should write tutorials instead. The value of a book is not more than the sum of its parts. Response: let’s work on the vignettes and tutorials and then work them into a book eventually?
  5. Concern: duplicate material in the book?
  6. Some books have lasted a long time – would Cytoscape fit that mold?
  7. A lot of books stem from existing teaching material e.g. course notes, tutorials.
  8. Concern: the field is changing too quickly to capture in a book
  9. Concern: it is a huge amount of work
  10. Maybe we just need to focus our publishing excitement on writing a series of papers. General agreement about this.
  11. Also, new forms of publishing e.g. publish Cytoscape session to the web, publish a Cytoscape 3.0 workflow to a blog, a tutorial, or the web. What venues are we not reaching, like social networking sites? E.g. twitter.

CytoscapeRetreat2008/Book (last edited 2009-02-12 01:03:00 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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