Covering the bioinformatics niche and much more

Preliminary Review of Python for Bioinformatics by Sebastian Bassi

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Let me start by saying that Python for Bioinformatics (Chapman & Hall/Crc Mathematical & Computational Biology)image is a massive book, massive in a way that it contains a lot of material. I still didn’t have enough time to check everything, but I’m well into the first section of the book that gives an initial view of Python and how to program it. The initial section of the book is well written (I’m not going criticize the book in terms of good/poor English, as I’m not well qualified to do that), and gives a clear perspective on how to program Python for scientists, who are the main target demographic of the book. Of course, it always help to have some basic knowledge of command line shells, but the book also includes some explanations of IDLE and other Python-capable IDEs. I cannot say that I read this section with the enough care and attention, but what I can say is that you won’t miss a beat with PfB, as it has more material than I expected. I still have to start with the more advanced topics, like BioPython and so forth, what I plan to do in the coming month, and as I don’t have a lot of experience with BioPython, I’m looking forward to it. On the other hand I have a small-ish complaint, that maybe is more about style than substance. I don’t like the design of the book, the way the code interleaves with the text and the way the code explanations are presented. Most of the code blocks are followed by a careful explanation, but this explanation works as a figure label for the code block. That is quite annoying because there are too many stops in the text fluidity as one tends to lose attention to it (my case, not exactly everyone’s). Another minor detail is the use of “he” every time scientists are referred (one example is on page 3 on the second phrase of the introduction). The (politically) correct would be to use “he or she” or “she or he” (but that’s OK with me). I will try to post more complete reviews of the sections that I don’t master. I would also like to thank Sebastian for sending me a copy of the book. Reblog this post [with