Name: Bioinformatics with Python Cookbook
Author: Shane Brubaker
ISBN: 9781836642749

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Bioinformatics with Python Cookbook

Shane Brubaker

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Contributors
About the author
About the reviewers
Preface
Who this book is for
What this book covers
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Download the example code files
Conventions used
Sections
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How to Unlock
1 Computer Specifications and Python Setup
Technical requirements
Installing the required basic software with Anaconda
Installing the required software with Docker
Introduction to Jupyter Notebook
2 Basics of Data Manipulation
Using pandas to process vaccine-adverse events
Dealing with the pitfalls of joining pandas DataFrames
Reducing the memory usage of pandas DataFrames
3 Modern Coding Practices and AI-Generated Coding
Technical requirements
Using linting tools and style guides to write accurate, well-formed code
Writing a simple bioinformatics file parser using AI
Read alignment
Writing tests with AI-assisted coding
Code review with AI
4 Data Science and Graphing
Technical requirements
Understanding NumPy as the engine behind Python data science and bioinformatics
Introducing scikit-learn with PCA
K-means clustering
Exploring breast cancer traits using decision trees
Learning more about Matplotlib for chart generation
Building a UMAP using Seaborn
5 Alignment and Variant Calling
Technical requirements
Quality control for sequencing data
Tools for sequence manipulation
Sequence alignment with BWA
Variant calling with FreeBayes
6 Annotation and Biological Interpretation
Technical requirements
Parsing and filtering variant files
Annotating a prokaryotic genome
Interpreting variants on gene structures
Annotating proteins
7 Genomes and Genome Assembly
Technical requirements
Accessing genome assemblies
Working with graph genomes
Long-read assembly with Raven
Assessing genome quality with QUAST
8 Accessing Public Databases
Technical requirements
Accessing GenBank and navigating NCBI databases
Using the Sequence Read Archive
Using PDB and UniProt
9 Protein Structure and Proteomics
Technical requirements
Extracting information from PDB files
Computing molecular distances on a PDB file
Performing geometric operations
Animating proteins
Performing proteomics analysis
10 Phylogenetics
Technical requirements
Preparing a dataset for phylogenetic analysis
Aligning genetic and genomic data
Comparing sequences
Reconstructing phylogenetic trees
Playing recursively with trees
Visualizing phylogenetic data
11 Population Genetics
Technical requirements
Managing datasets with PLINK
Using sgkit for population genetics analysis with xarray
Exploring a dataset with sgkit
Analyzing population structure
12 Metabolic Modeling and Other Applications
Technical requirements
Metabolic modeling with COBRApy
Designing siRNAs with BioPython and ViennaRNA
Predicting food properties using bioinformatics
Discovering genes to make novel molecules
13 Genome Editing
Technical requirements
Designing guide RNAs for genome editing
Counting barcodes in a genomic library
Using nanopore data to resolve genome edits
14 Cloud Basics
Technical requirements
Setting up an AWS account
Building cloud components using boto3
Building a container in AWS ECR
15 Workflow Systems
Technical requirements
Introducing Galaxy
Writing a bioinformatics workflow with Snakemake
Writing a bioinformatics workflow with Nextflow
16 More Workflow Systems
Technical requirements
Building a bioinformatics workflow with Flyte
Launching a bioinformatics orchestrator with AWS Step Functions
17 Deep Learning and LLMs for Nucleic Acid and Protein Design
Technical requirements
Machine learning with PyTorch
Designing proteins with LLMs
Designing DNA with LLMs
18 Single-Cell Technology and Imaging
Technical requirements
Building microfluidics devices
Analyzing single-cell data
Studying biological image data
Mapping the brain
19 Unlock Your Exclusive Benefits
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Bioinformatics with Python Cookbook