Cytoscape book discussion

Date: Friday, July 18, 2008

Description

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.

At the same time, we could present developer commentary in some form that helps (core, plugin) developers understand how to develop Cytoscape for end-users..

Agenda

• Item 1
• Item 2

Notes