Cytoscape_Book

TableOfContents([2])

Proposal

Publish a co-authored book on Cytoscape and its role in exploring biological networks as a companion to 3.0 release.

Background

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

Use Cases

The book would be oriented towards practitioners (users and developers) and would be a complement to the Cytoscape User Manual. Rather than being a how-to book, this would be more of a what is possible book. That is, each

Implementation Plan

Outline and describe the process and major issues related to implementing this proposal. Illustrate your plan when possible. Try this free online tool for making diagrams -> [http://www.best4c.com/editor/NetMapApplication.jsp Best4c] (draw; save; then insert hyperlink into this page)

Project Management

Project Timeline

Provide a timeline for implementation. Insert a graphic if you can. Try this free online tool for making project timelines -> [http://www.helpuplan.com/index.asp Help-u-Plan] (create a new chart; modify; right-click to save gif; then attach to this page)

Tasks and Milestones

Outline the major milestones and tasks involved in implementation.

1. Milestone 1: …

   1. Task 1: ...
   2. Task 2: ...

2. Milestone 2: …

Project Dependencies

Outline and projects that depend on this project, link to relevant RFC's and note at what point dependent projects could be started.

Related RFCs

Link to other related RFCs

Issues

1. What is the right venue for publishing -- traditional publisher, Publish-on-Demand service, WikiBook?

Comments

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