good introduction to new users,
This review is from: Instant Cytoscape Complex Network Analysis How-to (Paperback)
I used Cytoscape during the 1st year of my PhD several years ago, but since then I hadn't touched it. I recently needed it again for a network biology project and this book served as a reference to refresh my original training.
This book will not teach you network biology, bioinformatics, or graph theory however it provides a comprehensive introduction to the basic functions of the Cytoscape software package to begin building and visualising networks. The book assumes no previous experience of Cytoscape and provides an easy introduction to installing the software on Windows, Mac, and Linux as well as configuring it to access local and web based data sources. The language of the book is relaxed and illustrated with screen shots of the Cytoscape interface and the various graphic outputs.
The text uses sample data files, packaged with the Cytoscape installation as example material that the reader can work along with. Using these example networks, the user is shown how to import data, modify nodes and edges, customise the layout and graphics, and provides overview of the various layout algorithms.
The author structures the material into a beginner section, covering graphical changes to node, edges, and layouts. An intermediate section covers plugins for additional tools such as search tools and some layout plugins, and moves onto an advanced section covering some clustering and network topology plugins. There is also an overview of obtaining networks and ontology data from online databases such as entrez, and how to link out to literature sources to begin annotating the network. For those who have used some bioinformatics web based tools, and have used software with extensions, or plugins these sections are not challenging. The material retains the same simple explanations and illustrations to cover all of the material without requiring too much bioinformatics training.
Cytoscape has recently moved to version 3 which has been a significant overhaul of version 2. The book is written for Cytoscape 2, and I had initially wondered why the author had not covered version 3. For basic Cytoscape functionality I was able to follow all of the material in the book and apply it to version 3. Many of the plugins however have not been ported to version 3, and I rolled back to version 2 in order to use the additional plugin functions covered by the author. For my own work I think will remain with version 2 until the plugin community catches up.
While this book is very basic in it's material, the author outlines the use of a number of 3rd party (free) plugins which are available from either the plugin manager inside the software, or from Cytoscape.org. I found this content to be particularly useful, as there are a number of plugins available and it is not always obvious which ones add what functionality, or how to use them. The author includes a number of plugins which are generally useful and extend the capabilities of the base Cytoscape installation significantly, in terms of additional layout algorithms and cluster analysis.
I would have liked to have seen some additional material on the network analysis tool, in terms of gaining more detailed understanding of the network structure, and how it can be interpreted by a biologist looking for a hypothesis. It would have been useful to have had exercises at the end of the sections that could be built up into a mini-project around the text, taking some basic published network and performing analysis to make a conclusion about the network topology for some experimentally testable hypothesis. As the book stands however, it provides a handy cookbook for quickly getting Cytoscape up and running, visualising a network, customising the graphics, and populating it with data.
There are many tutorials available on the internet for Cytoscape, and if you want to save a few pounds then hunt them out. However, this book provides a handy collection of plugins and easy to follow tutorial material to understand how they work, and to build up a useful collection from the start. I would not recommend this book to anybody who feels comfortable using Cytoscape already, or has had formal bioinformatics training, but for a biologist who is is considering their first time experience of network visualisation then I think this book would be quite useful and easy to access.