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Instant Cytoscape Complex Network Analysis How-to, by Gang Su
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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.
Approach
Filled with practical, step-by-step instructions and clear explanations for the most important and useful tasks. Get the job done and learn as you go. A how-To book with practical recipes accompanied with rich screenshots for easy comprehension.This How-to guide offers techniques and skills through recipes. The guide is packed with step-by-step instructions for anyone who wants to learn to use Cytoscape for visualizing networks.
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.
- Sales Rank: #1752892 in eBooks
- Published on: 2013-03-26
- Released on: 2013-03-26
- Format: Kindle eBook
About the Author
Gang Su is a PhD candidate in Bioinformatics at the University of Michigan. He has also an MA in Statistics and an MS in Biochemistry and Molecular Biology. He began to engage in the Cytoscape community in 2008, when he first participated in the Google Summer of Code (GSoC) and accomplished a Cytoscape plugin project. He then co-mentored and mentored students for Cytoscape GSoC projects for the following three years. He has extensive working experience with Cytoscape, and developed several Cytoscape plugins for network visualization, clustering, and attribute search.
Most helpful customer reviews
0 of 0 people found the following review helpful.
Reasonable price/content ratio
By Egon Willighagen
Copied from [...]
Instant Cytoscape Complex Network Analysis How-to (ISBN:978-1-84951-980-9) is a book by Gang Su and reviewed by John Morris, which currently costs less than 10 euro. It is a thin book, with a mere 76 pages of which 58 pages are really informational. Of those pages, a lot of space is taken up by screenshots, which you may or may not like.
In the ten chapters of the book, it does give a concise introduction to Cytoscape. It is clearly written and easy to digest. The chapter titles read as follows, giving you an idea of the topics it covers:
Unboxing Cytoscape (easy), Loading up Cytoscape! (easy), Touch Cytoscape with some style, A network with many forms, Finding needles in a haystack, Tuning up Cytoscape with gadgets, Where are the clusters? (advanced), Additional visualization capabilities, When local is not enough, Export, save, and call it a day!
The qualification of easy and advanced looks somewhat arbitrary. I would guess for many scholars, installing the software may in fact be more difficult than pushing some buttons to do a cluster analysis. Otherwise, the book is targeted at people whit basic programming knowledge, network analysis, and Cytoscape usage. The requirements do not list that MS-Windows is needed, but assumes that is the case. That puts OS/X and Linux users at a disadvantage, particularly with the installation chapter.
The [PACKT] publishers provides the book in various formats, and I mostly read the PDF version. I did have a quick look at the EPUB version. Compared to PDF this format has the advantage the text shown will scale to fit the device, whereas a PDF page is always the same. Unfortunately, this version lost some layout aspects, leading to confusing text, badly shown URLs, and only partly shown screenshots in the Aldiko Book Reader. But because whitespace is one of the important things, I would recommend the PDF. However, you can download it in multiple formats, making this a smaller issue.
Each chapter consists of one or more sections called "Getting started", "How to do it...", "How it works...", "There's more...", "See also". Practically, however, you run through a chapter on one go, perhaps also, because of the (limited) length of chapters. I would very much recommend more of the "There's more..." extended from small hints to full texts, giving the book both more mass and the author more justice.
In fact, compared to tutorials available online, the book mostly provides the convenience of having the information in a nice narrative. However, things that a book should provide too is an index, but that is missing from the book. I know I can use ^F too, but that is not entirely the same thing. An index has more power in guiding the user the the right section of the book. That is, when I browse an index, I see other words the author found important. It is like a table of content, and chapter titles you can also find with ^F after all.
The examples are easy to follow, and assuming Cytoscape 2.8 does not change a lot within one series, we can assume the screenshots and instructions will not change. That is always the risk with a book like this. I hope the book will see frequent extensions and updates.
There were a few things that I had trouble with. One thing is the lack of distinction between Open Source and free of cost. Those are not the same thing. So, rather than writing "It is open source (free of cost)..." I would very much prefer it to read "It is open source and free of cost...". Also, a categorization of MS-Excel as a text editor is awkward, and I hope the next edition will also use OpenOffice/LibreOffice as replacement which is way more in line with the "It is open source..." introduction in the first place.
Content wise, I think the book is fairly solid and it surely covers all the basics one may want to do. A few plugins are mentioned, though they are a bit hidden. I would very much like to see a few plugins appear as separate (advanced?) chapters as show cases for who all that basic functionality is put to use. This is in parallel with the "there is more" sections, which could refer to such chapters. A bit of work, but it would make the book a lot more valuable and go beyond the basic tutorial nature it has now.
All in all, I think the book has a very reasonable price/content ratio and combined with the fact that some environments live by if-it-is-not-in-the-library-it-does-not-exist, I can recommend to keep an eye out for this book. Perhaps wait for the next edition, adding at least an index, but it is an easy and cheap way to support and encourage the Cytoscape community.
Oh, and while composing the below CiteULike widget, I realized that the book lacks references to other literature. For example, there is no reference to the Cytoscape articles. That would be another way to add value over the online tutorials.
0 of 0 people found the following review helpful.
Nice beginner's book for cytoscape
By ping
I like this beginner's book. It started with the basic functions of Cytoscape, how you load files, link data and annotations, change style and layout, how to search and filter data. It then covered the plugins (app), installation, examples of layout plugins (Layout SaverPlugin, World Cloud, FM3), cluster plugins (MCODE, ClusterOne, ClusterMaker, Community cluster/Glay, Hierarchy Cluster, K-Means Cluster), data visualization plugins (VistaClara, CyAnimator, lgraphPlugin). It also talked about how to import data from variety of public resources, such as NCBI Entrez Gene, Agilent LiteratureSearch MiMl, and how to save and share the file.
I also like the author mentioned in each chapter about what is extra, for example, what other packages or extra readings you can explore by yourself, beyond cytoscape, what other graph packages you can use.
The whole book is based on Cytoscape 2.8. Author mentioned a little bit on the differences of Cytoscape 3 and the version issue. It will be nice that this book can go a little bit further on some details regarding this and explain a little bit on the development environment. Also it might be beneficial to talk about how you build a network from scratch. ebook web site: ([...]
0 of 0 people found the following review helpful.
Recommended to cytoscape novices
By Spheromics
Gang Su has drafted a very fine,comprise beginner's guide through the possibilities which the software package Cytoscape offers for pathway and network analysis of biological data, such as gene expression studies. The composition of the chapters and the language Gang uses simplify getting acquainted with the subtleties of analyses, and provide a clear guidance. As the author points out in the book, a new version of Cytoscape has been released during the publication phase of the book, such that a lot of the information in the book will need to be revised in a further edition.
For everyone else, there is the Help-page within the software package.
[...]
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