Prologue
1 Getting started with Python Setting yourself up to use Python
2 Python at the lab bench The fundamentals of the Python language
3 Making sense of sequences  Biological sequences and Python data structures
4 A statistical interlude Of Bayes theorem and biomarkers
5 Opening doors to your data Reading, parsing and handling biological data files
6 Finding needles in haystacks Regular expressions for genomics and sequencing
7 Object lessons  Biological sequences as Python objects
8 Slicing and dicing genomes Next-generation sequencing pipelines
9 The wells! The wells!  Microtiter plate assays I: data structures
10 Well on the way Microtiter plate assays II: automation and visualization
11 Molecules in 3D Mathematics and linear algebra for structural biology
12 Turning genes on and off Visualizing biochemical kinetics using matplotlib
13 Taming the network hairball Using Python sets to mine systems biology data
14 Genetic feedback loops Modeling gene networks with the Gillespie algorithm
15 Growing a virtual garden  Modeling plant development with L-systems
16 How the leopard got its spots Cellular automata models of Turing patterns
17 Foxes guarding henhouses Ecological modeling with predator-prey dynamics
18 A virtual flu epidemic Exploring epidemiology with agent-based models
19 Retracing life’s footsteps Evolutionary dynamics with the Wright-Fisher model
Epilogue