/CompBiol3

Computational Biology Book 3rd Edition

Primary LanguageJupyter NotebookGNU General Public License v3.0GPL-3.0

CompBiol3

The magic juggler presents ...

... repository for my book "Computational Biology - A Practical Introduction to Bio Data Juggling with Worked Examples", 3rd Edition, 2024

About this Repository

The folders are numbered in the same way as the chapters in the book are numbered:

  • 05_TheBash -> Working with Files
  • 07_TextEdit -> Playing with Text and Data Files
  • 08_ShellUse -> Get More Out of the Shell
  • 10_ShellPrg -> Shell Programming
  • 11_RegEx -> Regular Expressions
  • 12_Sed -> Sed
  • 13_AWK -> AWK
  • 16_MariaDB -> Relational Databases with MariaDB
  • 17_RStudio -> The Statistics Suite R
  • 18_PrimerBlast -> BLASTing Forensic PCR Primers
  • 19_Pathogenicity -> In Search of Differences in Proteomes
  • 20_Sequencing -> Virtual Sequencing of mtDNA
  • 21_NanoporeSeq -> DNA Sequence Analysis of MinION Nanopore Reads
  • 22_Thioredoxin -> Querying for Potential Redox-Regulated Enzymes
  • 23_SARS-CoV-2 -> Exploring Early SARS-CoV-2 Mutations
  • 24_GWAS -> Genome-Wide Association Studies (GWAS)

About the Book

This extensively expanded 3rd edition offers a practical introduction to Bio Data Science. With a hands on-approach to learning, this book offers ample opportunity to practice:

  • Installing and utilizing Linux as a virtual machine or remotely
  • Processing bio data with the programming language AWK
  • Managing data with the relational database system MariaDB
  • Analyzing and visualizing data with R
  • Implementing good bioinformatics practices with Jupyter Notebook and GitHub

This book targets students and professionals in life sciences. While aimed at beginners, it also offers valuable tips and tricks for experienced researchers dealing with large datasets.

Worked examples illustrate how to utilize various bioinformatics tools such as BLAST, Clustal, PLINK, IGV, SAMtools, BCFtools, Mason2, Minimap, NCBI Datasets, Velvet, Jmol, and more for:

  • Identifying bacterial proteins potentially associated with pathogenicity
  • Querying molecular structures for redox-regulated enzymes
  • Mapping and assembling real or simulated sequence reads
  • Identifying and mapping molecular structure mutations in viruses
  • Conducting genome-wide association studies

All software tools and datasets mentioned are freely available. Drawing from the author's experiences and knowledge gained from both academia and industry, this book provides a practical and comprehensive approach to bioinformatics.

You will find more information about the book at SpringerNature