Sunday, May 12, 2013

Book Review: "Instant Cytoscape Complex Network Analysis How-to"

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 how 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.

Su, G. Instant Cytoscape Complex Network Analysis How-to (2013). ISBN:978-1-84951-980-9.