Digital library
Textbooks, references and open learning resources.
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A Primer for Computational Biology
Shawn O'Neil · Oregon State University · 2017
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: 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. 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. 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.
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Quantitative Problem Solving in Natural Resources
Pete Moore · Iowa State University Digital Press · 2025
This book is a collection of resources focused on solving quantitative problems that non-mathematicians interested in biology and environmental sciences may find compelling. It is not intended as a guide to be followed through a series of skills, but rather as a resource to support the problem-solving process and help lower conceptual and computational barriers along the way.
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Think Complexity: Exploring Complexity Science with Python
Allen Downey · Green Tea Press · 2018
Complexity science uses computation to explore the physical and social sciences. In Think Complexity, you'll use graphs, cellular automata, and agent-based models to study topics in physics, biology, and economics. Whether you're an intermediate-level Python programmer or a student of computational modeling, you'll delve into examples of complex systems through a series of worked examples, exercises, case studies, and easy-to-understand explanations. In this updated second edition, you will: Work with NumPy arrays and SciPy methods, including basic signal processing and Fast Fourier Transform Study abstract models of complex physical systems, including power laws, fractals and pink noise, and Turing machines Get Jupyter notebooks filled with starter code and solutions to help you re-implement and extend original experiments in complexity; and models of computation like Turmites, Turing machines, and cellular automata Explore the philosophy of science, including the nature of scientific laws, theory choice, and realism and instrumentalism Ideal as a text for a course on computational modeling in Python, Think Complexity also helps self-learners gain valuable experience with topics and ideas they might not encounter otherwise.