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Python for Bioinformatics [Paperback]

Sebastian Bassi
5.0 out of 5 stars  See all reviews (1 customer review)
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Book Description

Sept. 30 2009 1584889292 978-1584889298 1

Programming knowledge is often necessary for finding a solution to a biological problem. Based on the author’s experience working for an agricultural biotechnology company, Python for Bioinformatics helps scientists solve their biological problems by helping them understand the basics of programming. Requiring no prior knowledge of programming-related concepts, the book focuses on the easy-to-use, yet powerful, Python computer language.

The book begins with a very basic introduction that teaches the principles of programming. It then introduces the Biopython package, which can be useful in solving life science problems. The next section covers sophisticated tools for bioinformatics, including relational database management systems and XML. The last part illustrates applications with source code, such as sequence manipulation, filtering vector contamination, calculating DNA melting temperature, parsing a genbank file, inferring splicing sites, and more. The appendices provide a wealth of supplementary information, including instructions for installing Python and Biopython and a Python language and style guide.

By incorporating examples in biology as well as code fragments throughout, the author places a special emphasis on practice, encouraging readers to experiment with the code. He shows how to use Python and the Biopython package for building web applications, genomic annotation, data manipulation, and countless other applications.


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Review

The book will be helpful for its intended audience. Numerous code fragments in the book will be beneficial for biologists who are unfamiliar with programming. Readers can try out, test, and modify the code to suit their needs. … a useful introduction to the topic. The style of presentation is good, and the code samples are worthwhile. … I strongly recommend this book as a useful reference for computational biologists, programmers, and bioinformatics specialists (students as well as researchers).
Computing Reviews, November 2011

About the Author

Sebastian Bassi is the leader of the DNALinux bioinformatics distribution and member of the developer team for Biopython. He is currently providing bioinformatics support for the tomato mitochondrial genome sequencing project, which is part of the Latin America Solanaceae Genome Project (LAT-SOL). 


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Most helpful customer reviews
0 of 1 people found the following review helpful
5.0 out of 5 stars Valuable resource for Bioinformaticians April 26 2010
Format:Paperback
I can only say that I highly recommend this book, especially for the biologist that is beginning in bioinformatics or python (or both). I cannot compare it to any other Python and Bioinformatics books (I'm planning to buy the another one), but I can say that I could learn a thing or two from Sebastian's book. Evidently is not a perfect book, as some of the explanations are a little bit rushed and might be difficult for a beginner. At the same time this is a very carefully thought and planned book and has more than enough for one to learn Python and apply the language to solve biological problems. I really liked the BioPython section, and this section made me use BioPython for the first time. Some of BioPython's examples in the book are light years ahead of the examples in the tool's website.

Lastly, I would like to congratulate Sebastian for his work and effort in putting together a nice tome for Python and Bioinformatics. It's a valuable resource for everyone in the field and certainly will help spread Python in the community.
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Amazon.com: 4.2 out of 5 stars  5 reviews
6 of 6 people found the following review helpful
5.0 out of 5 stars Valuable resource April 26 2010
By Paulo Nuin Suano - Published on Amazon.com
Format:Paperback
I can only say that I highly recommend this book, especially for the biologist that is beginning in bioinformatics or python (or both). I cannot compare it to any other Python and Bioinformatics books (I'm planning to buy the another one), but I can say that I could learn a thing or two from Sebastian's book. Evidently is not a perfect book, as some of the explanations are a little bit rushed and might be difficult for a beginner. At the same time this is a very carefully thought and planned book and has more than enough for one to learn Python and apply the language to solve biological problems. I really liked the BioPython section, and this section made me use BioPython for the first time. Some of BioPython's examples in the book are light years ahead of the examples in the tool's website.

Lastly, I would like to congratulate Sebastian for his work and effort in putting together a nice tome for Python and Bioinformatics. It's a valuable resource for everyone in the field and certainly will help spread Python in the community.
3 of 3 people found the following review helpful
5.0 out of 5 stars Complete, detailed, intelligent Dec 30 2011
By Allan Lindh - Published on Amazon.com
Format:Paperback
This should not be your first python book, for that use "How to think like a computer scientist, Python version", which is available free online. But as the next book this one beats the heck out of any of the others I've tried, especially if Bioinformatics is your primary interest. Strives for logical completeness in his presentation of Python's features, unlike most books which give you a grab-bag. Approximately one zillion typos and errors in the English text, but who cares -- his code seems to be very tight, and all is available online. This is not Python for Idiots, but is not an exercise in some author demonstrating what opaque code he can generate either. He strives for clarity and moving you forward in small steps -- doesn't always succeed, but at least tries. Exceptional programming language book -- there is a good reason the used price is same as new -- this is not a book you'll discard soon.
1 of 1 people found the following review helpful
3.0 out of 5 stars Good but not great June 5 2012
By E. Ferris - Published on Amazon.com
Format:Paperback|Verified Purchase
A good introduction to bioinformatics programming and BioPython. Not the clearest explanations and it is filled with typos. A helpful book overall, but not as smooth as it could be.
5.0 out of 5 stars AWESOME Dec 23 2013
By nico55 - Published on Amazon.com
Format:Paperback|Verified Purchase
this book helped me so much! learning python changed my life. and i would make this required material for any grad level biology student. knowing this language can help with everything. (accept spelling)
3.0 out of 5 stars Content is great, but edition I bought has typos July 27 2014
By Tragic City - Published on Amazon.com
Format:Paperback|Verified Purchase
Content is great, but edition I bought has typos. One of my students complained about the English not being correct. I've noticed other books from CRC seem to be poorly copy-edited. Which is too bad because the authors are often great - experts in their fields.
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