Book Title: A Primer for Computational Biology

Author: Shawn T. O’Neil

Book Description:

Now available in print at Amazon.com and via the OSU Press!

License:
Creative Commons Attribution NonCommercial ShareAlike

Contents

Book Information

Book Description

A Primer for Computational Biology aims to provide life scientists and students the skills necessary for research in a data-rich world. The text covers accessing and using remote servers via the command-line, writing programs and pipelines for data analysis, and provides useful vocabulary for interdisciplinary work. The book is broken into three parts:

  1. Introduction to Unix/Linux: The command-line is the “natural environment” of scientific computing, and this part covers a wide range of topics, including logging in, working with files and directories, installing programs and writing scripts, and the powerful “pipe” operator for file and data manipulation.
  2. Programming in Python: Python is both a premier language for learning and a common choice in scientific software development. This part covers the basic concepts in programming (data types, if-statements and loops, functions) via examples of DNA-sequence analysis. This part also covers more complex subjects in software development such as objects and classes, modules, and APIs.
  3. Programming in R: The R language specializes in statistical data analysis, and is also quite useful for visualizing large datasets. This third part covers the basics of R as a programming language (data types, if-statements, functions, loops and when to use them) as well as techniques for large-scale, multi-test analyses. Other topics include S3 classes and data visualization with ggplot2.

Author

Shawn T. O’Neil

License

Metadata

Title
A Primer for Computational Biology
Author
Shawn T. O’Neil
License

A Primer for Computational Biology by Shawn T. O’Neil was a collaboration between the Oregon State University Press, the OSU Library, and the OSU office of Open Educational Resources. It originated out of the Center for Genome Research and Biocomputing at Oregon State University.

Publication and on-going maintenance of this textbook is possible due to grant support from Oregon State University Ecampus.

Publisher
Oregon State University Press
Print ISBN
978-0-87071-926-4