RFC Name : Cytoscape Book

Editor(s): Allan Kuchinsky

Date: 2008-05-02

Status: <!>Under Construction

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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.

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 partitioned 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. (n.b. I am not completely happy with this particular partitioning into sections, would appreciate suggestions of other alternative partitioning).



Problem Description

Cytoscape Functionality




Provide vision and context. Describe the role of biological networks in understanding and curing disease, personalized medicine, etc.


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, GenMAPP

Network inference

inferring networks and interactions from expression data, non-structured text, clustering ...

Agilent Literature Search, use case in atherosclerosis?

Network editing and Curation

subnet extraction, cytoscape editor


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, Linkout


Exploring Networks

Overview of Information Visualization principles

zooming, birds-eye-view, hide-show, rendering/level of detail


Graph Layout

Overview of criteria and algorithms for aesthetic graph layout

Cytoscape Layouts

Mapping data to visual properties

Description of data coding


MSKCC expression viewer, dynamicXPR, VistaClara


managing network and data complexity via aggregation

Groups, network merge

clustering plugins


overview of information retrieval issues

Filters, QuickFind

Cytoscape ESP

Analyzing Networks


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 Analyzer plugin

identifying community structure

mCODE, GoSC normalized visualization project, jActiveModules

network comparison

network merge

functional enrichment

overview of biological ontologies

BiNGO, BubbleRouter

Perspectives and Conclusion

developer's perspective

how to write a cytoscape plugin

non-biological networks

social networks, telecoms network management

emerging standards


Molecular Interaction Maps

the future

personalized medicine, etc.

Project Management

Editors' responsibilities for preparatory phase

Here are some thoughts about the tasks/responsibilities of anyone serving as an editor or 'associate' editor during the preparatory phase, which would result in a report and recommendations to be presented at the 2008 Cytoscape retreat, plus an extended outline or rough draft version of the book with 'synopsis' versions of each chapter.

Project Timeline

Provide a timeline for implementation. Insert a graphic if you can. Try this free online tool for making project timelines -> 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.

Link to other related RFCs


  1. what are the primary and secondary audiences for the book
    1. students in bioinformatics courses?
    2. all molecular biology students?
    3. practitioners in pharma, government research, academic research?
    4. general interest to science-minded public?
  2. what type of book should it be?
    1. core textbook (aimed at 1st year or 2nd year undergraduates)
    2. a supplementary book (aimed at less commonly taught higher level courses and interested researchers)
    3. a monograph (based on original research and likely to be of interest only to fellow researchers in the field)
    4. a handbook (a large edited compendium of originally commissioned chapters)
  3. what are the competing titles?
    1. we should be able to name 2-3 competitor texts available, their strengths, weaknesses,
    2. how would our book differ?
    3. are we aware of other competitive titles that may be published in the next 1-2 years?
  4. What is the right venue for publishing -- traditional publisher, Publish-on-Demand service, WikiBook?

    1. todo: list advantages/disadvantages of each

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


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.

From annette adler:

Book Outline

Foreword: Lee Hood—on the origins of Cytoscape & the motivation, systems biology vision, the place now within systems biology, the future

Afterword: Ruedi Aebersold—on his lab’s pragmatic need for and use of Cytoscape (an interesting bookend to the visionary frontpiece). Place of Cytoscape within ETH

Structure of book:

1. 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.

2. But at another level, each case would be written so that end-user readers could see how *their* situation might ‘map’ to these cases in meta terms, apart from the particular, case-specific terms (disease, data type, etc)

For example (using Agilent case studies for illustrative purposes only) --Stanford CV Medicine case—would describe Allan & Aditya’s work with Stanford on melding GE from several array experiments, clinical data, combined with literature search-based networks into a ‘connectivity analysis’ that yielded an analysis that went beyond anything statistical analysis alone could have presented. At a meta level: single data type, literature search, subnetworks combined into a larger network to analyze ‘nexus’ points --SUNY Syracuse work—combined CGH, GE, genotyping data together into a single large network. Meta level: combining disparate data types

3. 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.

In the end, the book would not age-out—but would potentially be a guide for multiples types of readers:

1. new scientist end-users of Cytoscape, who could read the cases and find one close to their own situation and see how Cytoscape was used, in a fairly detailed but crisp description 2. students, for educational purposes 3. programmers, for educational purposes 4. programmers (core, plugins) helping end-users, to help them better understand end-users’ goals/needs—and potentially provide short-cuts in insights 5. Cytoscape 3.0 community, helping them—as they progress in the refactoring and in preparing this book—understand why Cytoscape exists—and potentially impact that refactoring (favorably) in the process

Cytoscape_Book (last edited 2009-02-12 01:04:00 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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