Name: Python for the Life Sciences
ISBN: 978-1-4842-4523-1

Authors:

Alexander Lancaster ⁰,
Gordon Webster ¹

Alexander Lancaster
1. Amber Biology, Cambridge, USA
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Gordon Webster
1. Amber Biology, Cambridge, USA
View author publications

You can also search for this author in PubMed Google Scholar

Brings together life science’s and Python programming
Covers how to find sequences, automate boring calculations, build models, and generally have fun doing quantitative research with Python.
Covers Python with examples drawn from real life science research in a fun, engaging style

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Table of contents (19 chapters)

Front Matter

Pages i-xxxvi

PDF
Getting Started with Python
- Alexander Lancaster, Gordon Webster
Pages 1-12
Python at the Lab Bench
- Alexander Lancaster, Gordon Webster
Pages 13-29
Making Sense of Sequences
- Alexander Lancaster, Gordon Webster
Pages 31-49
A Statistical Interlude
- Alexander Lancaster, Gordon Webster
Pages 51-60
Opening Doors to Your Data
- Alexander Lancaster, Gordon Webster
Pages 61-75
Finding Needles in Haystacks
- Alexander Lancaster, Gordon Webster
Pages 77-91
Object Lessons
- Alexander Lancaster, Gordon Webster
Pages 93-119
Slicing and Dicing Genomes
- Alexander Lancaster, Gordon Webster
Pages 121-145
The Wells! The Wells!
- Alexander Lancaster, Gordon Webster
Pages 147-179
Well on the Way
- Alexander Lancaster, Gordon Webster
Pages 181-206
Molecules in 3D
- Alexander Lancaster, Gordon Webster
Pages 207-228
Turning Genes On and Off
- Alexander Lancaster, Gordon Webster
Pages 229-245
Taming the Network Hairball
- Alexander Lancaster, Gordon Webster
Pages 247-262
Genetic Feedback Loops
- Alexander Lancaster, Gordon Webster
Pages 263-289
Growing a Virtual Garden
- Alexander Lancaster, Gordon Webster
Pages 291-301
How the Leopard Got its Spots
- Alexander Lancaster, Gordon Webster
Pages 303-315
Foxes Guarding Henhouses
- Alexander Lancaster, Gordon Webster
Pages 317-327
A Virtual Flu Epidemic
- Alexander Lancaster, Gordon Webster
Pages 329-344
Retracing Life’s Footsteps
- Alexander Lancaster, Gordon Webster
Pages 345-359

About this book

Treat yourself to a lively, intuitive, and easy-to-follow introduction to computer programming in Python. The book was written specifically for biologists with little or no prior experience of writing code - with the goal of giving them not only a foundation in Python programming, but also the confidence and inspiration to start using Python in their own research.

Virtually all of the examples in the book are drawn from across a wide spectrum of life science research, from simple biochemical calculations and sequence analysis, to modeling the dynamic interactions of genes and proteins in cells, or the drift of genes in an evolving population.

Best of all, Python for the Life Sciences shows you how to implement all of these projects in Python, one of the most popular programming languages for scientific computing. If you are a life scientist interested in learning Python to jump-start your research, this is the book for you.

What You'll Learn

Write Python scripts to automate your lab calculations

Search for important motifs in genome sequences

Use object-oriented programming with Python

Study mining interaction network data for patterns

Review dynamic modeling of biochemical switches

Who This Book Is For

Life scientists with little or no programming experience, including undergraduate and graduate students, postdoctoral researchers in academia and industry, medical professionals, and teachers/lecturers.

“A comprehensive introduction to using Python for computational biology... A lovely book with humor and perspective”

-- John Novembre, Associate Professor of Human Genetics, University of Chicago and MacArthur Fellow

“Fun, entertaining, witty and darn useful. A magical portal to the big data revolution” -- Sandro Santagata, Assistant Professor in Pathology, Harvard Medical School

“Alex and Gordon’s enthusiasm for Python is contagious”

-- Glenys Thomson Professor of Integrative Biology, University of California, Berkeley

Keywords

Python
Bioinformatics
Computional Biology
Simulation
Biological Sequence
Python Objects
Genomic data
matplotlib library
Gillespie algorithm

Authors and Affiliations

Amber Biology, Cambridge, USA

Alexander Lancaster, Gordon Webster

About the authors

Alex Lancaster is an evolutionary biologist, engineer, writer and consultant. Alex completed his Ph.D. in evolutionary biology at the University of California, Berkeley, and also holds bachelor's degrees in physics and electrical engineering. He has worked in research & development in both Australia and the United States with a major focus on evolutionary and systems biology. He has also worked extensively in genomics, analyzing next-generation sequencing data and has developed tools for clinical and population genomics, with a particular specialization in immunogenetic applications. He has held research and faculty positions in academia, as well as R&D positions in the broadcasting and IT industries.

Alex has published many peer-reviewed papers and is interested in solving problems in biology using evolutionary and complex adaptive systems approaches. He has done pioneering work in this area as a co-developer of the open-source agent-based modeling toolkit, Swarm, one of the first tools for large-scale modeling of collective behavior in biology and beyond. He is passionate about the power of open source and open science approaches to accelerate discovery.

Gordon Webster has a PhD in biophysics and structural biology from the University of London, Gordon has worked in life science R&D in both Europe and the U.S., with a particular emphasis on molecular engineering and computational biology. In academic and commercial environments ranging from universities and medical schools to small venture capital-funded startups and global pharmaceutical companies, he has served in a diversity of roles from research faculty to company vice president.

Gordon is the author of numerous original scientific articles and patents and has created and managed some very successful research partnerships with industrial, academic and government organizations. He initiated and managed the first translational oncology clinical trial at a multinational pharmaceutical company and has coached and led research project teams in large matrix organizations, as well as large, distributed teams of scientists. software developers and technical specialists, working together across multiple time zones.

Gordon’s career path has always reflected his belief that the most interesting and potentially promising areas of research lie at the intersections between the traditional scientific disciplines.

Bibliographic Information

Book Title: Python for the Life Sciences
Book Subtitle: A Gentle Introduction to Python for Life Scientists
Authors: Alexander Lancaster, Gordon Webster
DOI: https://doi.org/10.1007/978-1-4842-4523-1
Publisher: Apress Berkeley, CA
eBook Packages: Professional and Applied Computing, Professional and Applied Computing (R0), Apress Access Books
Copyright Information: Alexander Lancaster and Gordon Webster 2019
Softcover ISBN: 978-1-4842-4522-4Published: 28 September 2019
eBook ISBN: 978-1-4842-4523-1Published: 27 September 2019
Edition Number: 1
Number of Pages: XXXVI, 376
Number of Illustrations: 116 b/w illustrations, 47 illustrations in colour
Topics: Python, Open Source