Python For Bioinformatics (Series in Biomedical Informatics) [Paperback]

Jason Kinser (Author)

Book Description

ISBN-10: 0763751863 | ISBN-13: 978-0763751869 | Publication Date: June 16, 2008 | Edition: 1

Bioinformatics is a growing field that attracts researchers from many different backgrounds who are unfamiliar with the algorithms commonly used in the field. Python for Bioinformatics provides a clear introduction to the Python programming language and instructs beginners on the development of simple programming exercises . Ideal for those with some knowledge of computer programming languages, this book emphasizes Python syntax and methodologies. The text is divided into three complete sections; the first provides an explanation of general Python programming, the second includes a detailed discussion of the Python tools typically used in bioinformatics including clustering, associative memories, and mathematical analysis techniques, and the third section demonstrates how these tools are implemented through numerous applications.

Product Details

• Paperback: 417 pages
• Publisher: Jones & Bartlett Publishers; 1 edition (June 16, 2008)
• Language: English
• ISBN-10: 0763751863
• ISBN-13: 978-0763751869
• Product Dimensions: 10 x 7 x 0.9 inches
• Shipping Weight: 1.7 pounds (View shipping rates and policies)
• Average Customer Review: 4.3 out of 5 stars  See all reviews (3 customer reviews)
• Amazon Best Sellers Rank: #444,022 in Books (See Top 100 in Books)
  • #60 in Books > Professional & Technical > Professional Science > Biological Sciences > Bioinformatics

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Customer Reviews

Most Helpful Customer Reviews

6 of 6 people found the following review helpful:

5.0 out of 5 stars A very well done book on implementing algorithms in Python, December 20, 2009

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calvinnme - See all my reviews
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This review is from: Python For Bioinformatics (Series in Biomedical Informatics) (Paperback)

The author is a well-liked professor at George Mason University, and he has been teaching bioinformatics programming from beginning to advanced for several years. This book is formed somewhat like his lectures for those classes. He assumes you have a background in bioinformatics and that you already know some Python. From there he goes on to show you many of the problems you may be faced with in bioinformatics coded in Python. He actually says that he is trying to answer the question most commonly asked by his students - "How do I put what you just taught into code?".

If you need to a good book on bioinformatics algorithms that is language agnostic may I suggest An Introduction to Bioinformatics Algorithms (Computational Molecular Biology) as well as Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. The latter book is especially good for computer science students seeking bioinformatics knowledge. Let me also point out that this book is of use for people seeking Python solutions to non-bioinformatics problems. Since much of bioinformatics has to do with dealing with strings, trees, and statistical analysis of data, students of subjects other than biology can find uses for this book.

Do note that the book's one great problem is that it is using Python 2 not Python 3. It is the fault of the designers of Python that most everything written for Python 2 becomes broken in a Python 3 interpreter rather than the fault of this author, yet the problem remains. Fortunately, Python looks enough like pseudocode that you can probably do any translations necessary without too much hair-pulling.

5 of 5 people found the following review helpful:

5.0 out of 5 stars Good book, but learn python first., September 18, 2009

By 

gani999 (Grenoble, France) - See all my reviews

This review is from: Python For Bioinformatics (Series in Biomedical Informatics) (Paperback)

Python isn't as popular as some other languages amongst bioinformaticans , but it is probably gaining acceptance and this book is a result of it. The author is a practising bioinformatician. This is a good book. It discusses all the mathematical concepts that bioinformaticians usually use, and how they can be implemented in python. It requires, as the author himself says, a fairly good knowledge of mathematics and basic molecular biology. In my opinion, it also requires a good familiarity with the python language. There is a very small introduction to it in the first chapter but beginners will need more exposure to the language than that. Since I can code in python, and I needed a book that jumped straight into the bioinformatics part, I like it.

3 of 4 people found the following review helpful:

3.0 out of 5 stars Could be better, November 19, 2010

By 

Software Engineer (Iowa, United States) - See all my reviews

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This review is from: Python For Bioinformatics (Series in Biomedical Informatics) (Paperback)

To be honest, I bought this book before I realized that what was out there for bioinformatics. I started a new job, and I knew Python, but I didn't know much about bioinformatics. I was a little disappointed that this book merely references biopython, and doesn't utilize it or show people how to use it. Why not use the tools that are available? In a classroom setting, I guess I can understand why you would want students to learn from the ground up, but this book is essentially teaching people Python in a bioinformatics way. For example, why does the book show how to parse fasta files in Chapter 6. This is merely a lesson in file parsing - something you should know if you understand Python, and why show it if biopython already does this for you.

If you don't know much about Python or Bioinformatics, then this book is probably for you. If you have previous Python experience, I would skip this book.