Python for Bioinformatics
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.
The book have four main sections:
Why second edition?
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.
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.
Source at Github
Comments about second edition
"Second edition catches up new information, nice to have those new updates."
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