Biological Modeling is a free and open online course that I built while overseeing a team of several excellent students. The course, hosted at biologicalmodeling.org, takes learners on a short tour of modeling biological systems at multiple “scales” of molecular and cellular modeling, from the study of a single protein within the cell’s cytoplasm, to a much wider view of cellular interactions. Each chapter poses a single biological question, from why zebras have stripes, to how bacteria explore their world intelligently, to why the SARS-CoV-2 spike protein was so effective at binding to human cells. The course then introduces the modeling concepts needed to answer this question, and it guides learners through applying real software to do so.

Biological Modeling features software tutorials from the National Center for Multiscale Modeling of Biological Systems consortium (MMBioS). As learners encounter each new topic, they are pointed to a tutorial using an MMBioS software resource that answers this question. In this way, the course constantly alternates between theory and practice.

If you are an instructor interested in adopting the materials for your own teaching, please contact me to let me know! I’m hoping to form a network of instructors using Biological Modeling.

Order the Biological Modeling Textbook

The course’s text companion, Biological Modeling: A Short Tour, is available in print form at Amazon and in electronic form at Leanpub. Some of the talented students at Carnegie Mellon University who helped build Biological Modeling appear in the book as chapter co-authors.

The publication of this textbook companion for Biological Modeling was crowdfunded at 210% of our campaign goal via Kickstarter and Indiegogo, receiving donations from 600 generous souls to whom I am forever grateful.

Contents

Biological Modeling is divided into a prologue and four modules of content, each of which focuses on a different aspect of biological modeling.

• Prologue: Random walks and Turing patterns (with software tutorials featuring MCell and CellBlender)
• Module 1: Finding motifs in transcription factor networks (with software tutorials featuring MCell and CellBlender)
• Module 2: Unpacking E. coli’s genius exploration algorithm (with software tutorials featuring BioNetGen)
• Module 3: Analyzing the coronavirus spike protein (with software tutorials featuring ProDy and affiliated tools)
• Module 4: Training a computer to classify white blood cells (with software tutorials featuring CellOrganizer)