Python for Biologists: A complete programming course for beginners

By | November 9, 2019
Python for Biologists: A complete programming course for beginners Author Dr Martin Jones
ISBN-10 1492346136
ISBN-13 9781492346135
Year 2013-09-07
Pages 244
Language English
Publisher CreateSpace Independent Publishing Platform
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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

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