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.
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.

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, in contrast to the User Manual and protocols articles we have published, which provide step-by-step directions for using the functionality, the book would provide technical background on the main problem areas for biological networks, coupled with descriptions of how Cytoscape and its plugins approach the problem area. The reader of the book would gain a knowledge of the state of research into biological network analysis and visualization, as well as some familiarity with the Cytoscape platform. The book would serve as a text and could potentially be used as a text for bioinformatics courses. The book could also serve as a general reference for Cytoscape, but the reader would be referred to the User Manual for specific details on how to use the functionality. This has the advantage of insulating the book from changes that will occur in ongoing releases of Cytoscape.

Implementation Plan

The following is one potential way of organizing the book. It could be organized into a small number of sections, each section oriented around a particular theme of network analysis and visualization and containing several chapters, each chapter oriented around a particular problem area, approach, or area of functionality. In addition to giving a survey of the problem area and describing the relevant Cytoscape functionality, the chapter could include sidebars on the relevant plugins and/or examples of real-world usage. Additionally, there would be introductory materials the provided vision and and overview of the area, also concluding materials that might describe future trends and how Cytoscape might evolve.

Following is an initial outline of potential sections, chapters, sidebars, and possible authors. It is not exhaustive. Please feel free to add or modify.

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?

2. Do we focus on biological networks or do we broaden the focus to include other kinds of networks?

Comments

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