## page was renamed from RFC Template
## This template should be used for creating new RFC's (Request for comments) for Cytoscape development
||'''RFC Name''' : Cytoscape Book ||'''Editor(s)''': Allan Kuchinsky ||'''Date''': 2008-05-02 ||'''Status''': <!>Under Construction ||
<<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, 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). ''
||'''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, Pathway''''''Commons, Bio''''''PAX, Gen''''''MAPP ||
|| ||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 ||Wiki''''''Pathways ||
|| ||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 ||Sub''''''Gene''''''Viewer? ||
||'''Exploring Networks''' ||Overview of Information Visualization principles || ||zooming, birds-eye-view, hide-show, rendering/level of detail ||Vista''''''Clara ||
|| ||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, dynamicXPR, Vista''''''Clara ||
|| ||Abstraction ||managing network and data complexity via aggregation ||Groups, network merge ||clustering plugins ||
|| ||Search ||overview of information retrieval issues ||Filters, Quick''''''Find ||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 Analyzer plugin ||
|| ||identifying community structure || || ||mCODE, GoSC normalized visualization project, jActiveModules ||
|| ||network comparison || ||network merge || ||
|| ||functional enrichment ||overview of biological ontologies || ||BiNGO, Bubble''''''Router ||
||'''Perspectives and Conclusion''' || || || || ||
|| ||developer's perspective ||how to write a cytoscape plugin || || ||
|| ||non-biological networks ||social networks, telecoms network management || || ||
|| ||emerging standards ||SBML, SBGN || ||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.

 * setting a baseline
  * surveying what books are out there, what are their strengths and gaps
  * gathering pointers to materials we can draw upon for our writing
   * familiarization: go through tutorials, wiki pages, Nature Protocols
 * learning and setting up the process
  * recruiting authors
  * contacting publishers
  * contacting, getting permission from people whose work we reference or summarize
  * explore different vehicles for publishing
 * project management
  * defining time line, dependencies, tracking tools and process
 * writing and editing
  * pulling together a synopsis on each of the technical areas for each chapter
  * excerpt information from user manual, Nature Protocols into Cytoscape-specific portion of each chapter
  * writing an excerpt chapter for submission with book proposal (should this be Overview chapter?)
  * consolidating peoples' different writing styles
  * pulling together sidebar articles for each chapter
 * book and page design
  * put together candidate cover designs
  * build/gather/position figures to go with the text
  * put together list of possible working titles
 * market research (see issues #1, 2, 3, 4 below)
=== Links to Publishers ===
 * wikibook http://en.wikibooks.org/wiki/Main_Page
 * publish on demand services http://www.createspace.com
 * Humana Press http://www.springer.com/humana+press?SGWID=0-146902-0-0-0
 * MIT Press, Author Services: http://mitpress.mit.edu/authors/default.asp
 * Sage Publications: http://www.sagepub.com/
 * Wiley: Authors page: http://www.wiley.com/WileyCDA/Section/id-301837.html
=== 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: ...
  1. Task 2: ...
 1. '''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 are the primary and secondary audiences for the book
  1. students in bioinformatics courses?
  1. all molecular biology students?
  1. practitioners in pharma, government research, academic research?
  1. general interest to science-minded public?
 1. what type of book should it be?
  1. core textbook (aimed at 1st year or 2nd year undergraduates)
  1. a supplementary book (aimed at less commonly taught higher level courses and interested researchers)
  1. a monograph (based on original research and likely to be of interest only to fellow researchers in the field)
  1. a handbook (a large edited compendium of originally commissioned chapters)
 1. what are the competing titles?
  1. we should be able to name 2-3 competitor texts available, their strengths, weaknesses,
  1. how would our book differ?
  1. are we aware of other competitive titles that may be published in the next 1-2 years?
 1. What is the right venue for publishing -- traditional publisher, Publish-on-Demand service, Wiki''''''Book?
  1. ''todo'': list advantages/disadvantages of each
 1. Do we focus on biological networks or do we broaden the focus to include other kinds of networks?
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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