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Python for Biologists
Why learn programming?
Maybe you see colleagues writing programs to save time and deal with large datasets.
Maybe your supervisor has told you that you need to learn programming for your next project.
Maybe you've been looking at job ads and noticed just how many of them are asking for programming skills.
Whatever your motivation, learning to program is one of the best investments that you can make for your research and your career. Python for biologists is a complete programming course for beginners that will give you the skills you need to tackle common biological and bioinformatics problems.
Table of contents>
In chapter one, you'll learn why Python is a good choice for biologists and beginners alike. You'll also learn how to install Python for your operating system and how to set up your programming environment, complete with links to all the free software you'll need.
In chapter two, you'll learn how to manipulate text (including DNA and protein sequences) and how to fix errors in your programs. Exercises: calculating AT content, splicing introns.
In chapter three, you'll learn how to read and write data to and from files. You'll also learn how to deal with file paths and the FASTA file format.Exercises: splitting genomic DNA, writing a FASTA file.
In chapter four, you'll learn how to process many pieces of data in a single program and more advanced tools for sequence manipulation. Exercises: trimming adapter sequences, concatenating exons.
In chapter five, you'll learn how to make Python even more useful by creating your own functions, including the best ways to test those functions in order to speed up development. Exercises: Analyzing the amino acid composition of protein sequences.
In chapter six, you'll learn how to write programs that can make smart decisions about how to handle data and how to make your programs follow complex rules. Exercises: filtering genes based on multiple criteria.
In chapter seven, you'll learn an incredibly powerful tool for working with patterns in text - regular expressions - and how to use it to search in DNA and protein sequences. Exercises: filtering accession names and calculating restriction fragment sizes.
In chapter eight, you'll learn how to store huge amounts of data in a way that can still allows it to be retrived very efficiently. This allows simplification of much of the code from previous chapters. Exercises: translating DNA sequences to protein.
In chapter nine, you'll learn how to make your Python programs work in harmony with existing tools, and how to polish up your programs so that they're ready for other people to use. Exercises: counting k-mers, binning DNA sequences by length.
About the author
Dr. Martin Jones has been teaching biologists to write software for over five years and has taught everyone from postgraduates to PIs. He is currently Lecturer in Bioinformatics at Edinburgh University.
Maybe you see colleagues writing programs to save time and deal with large datasets.
Maybe your supervisor has told you that you need to learn programming for your next project.
Maybe you've been looking at job ads and noticed just how many of them are asking for programming skills.
Whatever your motivation, learning to program is one of the best investments that you can make for your research and your career. Python for biologists is a complete programming course for beginners that will give you the skills you need to tackle common biological and bioinformatics problems.
Table of contents>
In chapter one, you'll learn why Python is a good choice for biologists and beginners alike. You'll also learn how to install Python for your operating system and how to set up your programming environment, complete with links to all the free software you'll need.
In chapter two, you'll learn how to manipulate text (including DNA and protein sequences) and how to fix errors in your programs. Exercises: calculating AT content, splicing introns.
In chapter three, you'll learn how to read and write data to and from files. You'll also learn how to deal with file paths and the FASTA file format.Exercises: splitting genomic DNA, writing a FASTA file.
In chapter four, you'll learn how to process many pieces of data in a single program and more advanced tools for sequence manipulation. Exercises: trimming adapter sequences, concatenating exons.
In chapter five, you'll learn how to make Python even more useful by creating your own functions, including the best ways to test those functions in order to speed up development. Exercises: Analyzing the amino acid composition of protein sequences.
In chapter six, you'll learn how to write programs that can make smart decisions about how to handle data and how to make your programs follow complex rules. Exercises: filtering genes based on multiple criteria.
In chapter seven, you'll learn an incredibly powerful tool for working with patterns in text - regular expressions - and how to use it to search in DNA and protein sequences. Exercises: filtering accession names and calculating restriction fragment sizes.
In chapter eight, you'll learn how to store huge amounts of data in a way that can still allows it to be retrived very efficiently. This allows simplification of much of the code from previous chapters. Exercises: translating DNA sequences to protein.
In chapter nine, you'll learn how to make your Python programs work in harmony with existing tools, and how to polish up your programs so that they're ready for other people to use. Exercises: counting k-mers, binning DNA sequences by length.
About the author
Dr. Martin Jones has been teaching biologists to write software for over five years and has taught everyone from postgraduates to PIs. He is currently Lecturer in Bioinformatics at Edinburgh University.
244 pages, Kindle Edition
First published September 7, 2013
11 people are currently reading
95 people want to read
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Displaying 1 - 6 of 6 reviews
April 10, 2020
This book is a great introduction to python! In the past, I have always struggled with learning Python because I felt like what was being taught was not applicable for what I wanted to use the program for. If you are a biologist struggling to learn how to code, I would definitely recommend this! The exercises at the end of each chapter successfully reinforces the lessons that were taught. My only critique of this book is that there were a few typos scattered throughout and the data file names in the book do not always match up with the appropriate data files that you would download from the website.
December 25, 2017
Great introduction! Well designed, useful exercises.
Only the 2nd book I've read on Python but definitely the best so far. Very excited to read the other 2 biology focused books by this author. My only other exposure to bioinformatics is through R, but Python is pretty great for some forms of data manipulation too, it seems!
Only the 2nd book I've read on Python but definitely the best so far. Very excited to read the other 2 biology focused books by this author. My only other exposure to bioinformatics is through R, but Python is pretty great for some forms of data manipulation too, it seems!
September 15, 2017
Perfect for getting started with Python using biological data.
January 29, 2021
Excelent book for biologist that want to start this new field of programming with python :D
Definitely, I will continue with the next book.
Definitely, I will continue with the next book.
June 12, 2021
Very clear introduction to python. It's suitable for any python beginners, not just for biologists.
November 4, 2015
If you want to learn Python to help you in Biology this is where you should start.
Displaying 1 - 6 of 6 reviews