Python for Bioinformatics

SECOND EDITION

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A solid introduction to programming with Python, accessible for readers without previous programming experience. Written for biologists, bioinformatics specialists and bench scientists in mind.

There were a lot of changes since the first edition was written in 2009. Enterprise attitude and support to Open Source Software in general and Python in particular has changed dramatically. Microsoft already support Python as a first class citizen in its Visual Code editor and in Azure. Current Python version is 3.8. Collaborative software development with Git and Github is the norm. Web development is another area that changed significantly over the last seven years. Frameworks replaced CGI/WSGI and middleware based applications. Apart from software evolution, the author gained development experience in a genome sequencing project at an international consortium and as a Senior Software Developer in a NYSE listed company.

  • Basic programming concepts, Installing Python, Interactive mode, Editors, Data types (Strings, Unicode, Lists, Tuples, Dictionaries, Sets), Flow control (If-Else, For, While), Functions, Generators, Modules, Using files including CSV and JSON and file operations, Error handling and Object Orienting Programming.
  • Biopython: Most important Biopython modules explained with sample usage.
  • A section with advanced topics such as: Web development (CGI and Bottle), XML, Databases (MySQL, SQLite and MongoDB), REGEX and Graphics (Bokeh).
  • Python recipes with commented source code.

The book have four main sections:


Book contents

Why second edition?

The author

Sebastián Bassi is a Biotechnologist with experience both in software development and bioinformatics research. He worked in a leader biotech company doing molecular marker database curation and in a national research institute helping with the bioinformatics support of the international effort to sequence the Tomato Genome. Both positions involved Python development and intensive data manipulation. He made a web application to query a micro RNA database, which was published at BMC Plant Biology. He also worked on the first Linux distribution for bioinformatics (DNALinux). He is an AWS Certified Solutions Architect and is frequently invited to Python conferences.

Sebastian's photo

Get the code


All code examples from the book are available from Github or as a Jupyter Notebook that can be run online.

Go to the book Github page and click on the green "Clone or download" button. The project includes all .py files ready to be executed locally and complementary files used in the book.





Jupyter logoGithub logo

Jupyter Notebook

Source at Github

Code can be run online at Microsoft Azure Notebook (free account is required). Jupyter notebooks (in .ipynb format) can also be downloaded from the Notebooks directory and run locally if you have Jupyter installed.




Comments about second edition

Kenneth

"Second edition catches up new information, nice to have those new updates."

Abhishek Kumar

Krishna S. Morampudi

"I really recommend this book for all aspiring Bioinformaticians. Older version of Bassi's book helped me a lot when I was learning and still use it for reference. I really appreciate all your efforts."

"A Necessary and Timely Upgrade of Python for Bioinformatics, as Second Edition" for Wiley Online Library

Python for Bioinformatics

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Second edition.