Cytoscape_Book - Cytoscape Wiki

RFC Name : Cytoscape Book

Editor(s): Allan Kuchinsky

Date: 2008-05-02

Status: <!>Under Construction

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:

a comprehensive and useful resource for the community of Cytoscape users and developers.
a comprehensive and useful resource for anyone who wanted to learn more about biological network analysis and visualization.
a way of broadening the user and developer base for Cytoscape.
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. I (AllanK) am likely to have forgotten major areas, so please help with additions, modifications, etc.

Section	Chapter	Problem Description	Cytoscape Functionality	Sidebars
Introductory	Forward	Provide vision and context. Describe the role of biological networks in understanding and curing disease, personalized medicine, etc.
	Overview	Describe the major problem and research areas of of Network Analysis, Visualization, and Data Integration. Give an overview of the sections and chapters of the book.
	User Perspective	Describe the work practices of different types of biomedical researchers and their needs from information technologies.		Describe a real-world use case that will be used as an example throughout the book.
Creating Content	Biological pathway resources and molecular interactions databases		web service clients, import networks from file/URLs	MiMI, PathwayCommons, BioPAX, GenMAP, WikiPathways
	Network inference	inferring networks and interactions from expression data, non-structured text, clustering ...		Agilent Literature Search, use case in atherosclerosis?
	Molecular Structure and Biochemical data	relation of biological networks to interactions at the molecular level -- domains, small molecule interactions		structureViz, GoSC cheminformatics plugin
	Data and Annotations		web service clients, import expression data, import attributes, import annotations
Exploring Networks	Overview of Information Visualization principles		zooming, birds-eye-view, hide-show	VistaClara
	Graph Layout	Overview of criteria and algorithms for aesthetic graph layout	Cytoscape Layouts
	Mapping data to visual properties	Description of data coding	vizmapper	MSKCC expression viewer, VistaClara
	Search	overview of information retrieval issues	Filters, QuickFind	Cytoscape ESP
Analyzing Networks	overview	description of main issues in network analysis, scale free networks, etc.
	graph-theoretic analysis	analysis of topological properties	nearest neighbor	GoSC random network generator
	network merge		Netwok merge	GoSC enhanced network merge projects
	identifying community structure			mCODE, GoSC normalized visualization project, jActiveModules
Perspectives and Conclusion
	non-biological networks	social networks, telecoms network management
	the future	personalized medicine, etc.

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.

Milestone 1: …
1. Task 1: ...
2. Task 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

What is the right venue for publishing -- traditional publisher, Publish-on-Demand service, WikiBook?
Do we focus on biological networks or do we broaden the focus to include other kinds of networks?

Comments

Add comment here…

How to Comment

Edit the page and add your comments under the provided header. By adding your ideas to the Wiki directly, we can more easily organize everyone's ideas, and keep clear records. Be sure to include today's date and your name for each comment. Try to keep your comments as concrete and constructive as possible. For example, if you find a part of the RFC makes no sense, please say so, but don't stop there. Take the extra step and propose alternatives.