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Python for Biologists: A complete programming course for beginners, by Dr Martin Jones
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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.
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.
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.
- Sales Rank: #47817 in Books
- Published on: 2013-09-07
- Original language: English
- Number of items: 1
- Dimensions: 9.69" h x .55" w x 7.44" l, .97 pounds
- Binding: Paperback
- 244 pages
Most helpful customer reviews
11 of 12 people found the following review helpful.
The most useful guide to Python I've found
By Katy
I'm currently working my way through this guide and am finding it enormously useful. I've tried a few Python books, and this is by far the best for me. It jumps straight into the things biologists generally need Python for - creating and manipulating sequence files for example. For all other guides I've tried, I've had to wade through chapters of less relevant material before I get to anything this useful. This book is also easy to read, the concepts are well explained, and the exercises at the end of the chapter are nicely challenging. I would definitely recommend this to any biologist.
9 of 10 people found the following review helpful.
Life-changing
By mypenname2126
Great, great book. I think this is the perfect book for any biologist to who wants to start learning to code with Python. Right away the author has you writing programs that are actually useful for biologists (making a reverse-compliment of a dna strand, calculating A-T content, finding restriction enzyme sites, ect). I didn't know a command-line from a hole in the ground when I first opened up this book, and mere days later I was impressing my colleagues with my own DNA analysis programs. I actually have this book to thank for easing me into programming which is now something I do everyday as part of my profession.This book is definitely unique for biologists in that it has you learning some aspects of python that are useful for biological applications right away- techniques which are normally several chapters down the road in general programming books. That being said, if you want to get serious about coding, because this book doesn't go over all areas of python, you will be well-served by also getting a second general python programming introduction book that goes over stuff this book does not cover.
6 of 6 people found the following review helpful.
Practical guide to programming
By jane e.
The order in which the programming language is presented and explained makes it directly usable and applicable to working in the biological sciences.
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