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Instant Cytoscape Complex Network Analysis How-to

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Gang Su

Use Cytoscape to import, search, annotate, visualize, and analyze networks
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Book Details

ISBN 139781849519809
Paperback76 pages

About This Book

  • Learn something new in an Instant! A short, fast, focused guide delivering immediate results.
  • Import and export networks using different formats
  • Use Vizmapper and layouts to customize the looks of your networks
  • Search for nodes and edges of interest

Who This Book Is For

This book is great for people who have basic knowledge of programming, network analysis, and Cytoscape usage but would like to visualize and explore some network data. Readers are expected to know the basic concepts of network data, and be capable of using text editing software to edit tabular data which is imported into Cytoscape. Optionally, the user should understand network clustering and command line tools such as R.

Table of Contents

Chapter 1: Instant Cytoscape Complex Network Analysis How-to
Unboxing Cytoscape (Easy)
Loading up Cytoscape! (Easy)
Touch Cytoscape with some style (Intermediate)
A network with many forms (Intermediate)
Finding needles in a haystack (Intermediate)
Tuning up Cytoscape with gadgets (Intermediate)
Where are the clusters? (Advanced)
Additional visualization capabilities (Intermediate)
When local is not enough (Intermediate)
Export, save, and call it a day! (Intermediate)

What You Will Learn

  • Use VizMapper to configure visual styles
  • Apply a variety of network layouts
  • Identify clusters for functional mapping
  • Search using complex criteria
  • Introduction to popular plugins
  • Access remote resources
  • Export and save your work

In Detail

Analyzing and visualizing networks for some of us has been quite difficult, although network typed data has been growing rapidly in almost all kinds of disciplines. Visualization of a network from its text or form can dramatically aid the intuitive human exploration and discovery of key features or functions. Cytoscape is a great tool for this purpose – no matter if you want to find out about a friendship group on Facebook or what a protein-protein interaction looks like.

Cytoscape Complex Network Analysis How-to is a hands-on book that provides you with step-by-step exercises to help you get familiar with Cytoscape. With the help of quick recipes, you will be able to load, visualize, search, cluster, import and export networks, and manage plugins without a hitch.

This book begins with an overview of the book (setup, basics, load networks), then progresses to VizMapper, layout and search functions, and concludes with plugins, clustering, remote services, and data export. Every recipe is designed very concisely to help you quickly get a general idea without diving into too much detail.

You will also learn how to build your own video player using jQuery, or by using one of the pre-built libraries available. We will also take a look at adding functionality such as lightbox effects, or subtitles, as well as how to publish videos to popular hosting sites, such as YouTube or VideoBin. If you want to take advantage of using the new HTML5 video format, then this is the book for you.

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