Pufferfish skin pattern showing Turing patterns Prologue
Random Walks and Turing Patterns
Why do zebras have stripes? Simple molecular interactions give rise to reaction-diffusion systems that spontaneously produce the complex, self-organized patterns found across the biological world.
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Repressilator oscillation chart Module 1
Finding Motifs in Transcription Factor Networks
Transcription factor networks exhibit recurring structural motifs, including oscillators, that appear too often to be coincidental. We'll model these patterns and ask why evolution keeps arriving at the same solutions.
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E. coli chemotaxis Module 2
Unpacking E. coli's Genius Exploration Algorithm
Bacteria navigate chemical gradients through a cascade of molecular reactions that produce robust, adaptive behavior. We'll construct a model of this system, introduce perturbations, and examine how the cell maintains its strategy.
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Coronavirus spike protein Module 3
Analyzing the Coronavirus Spike Protein
Why did SARS-CoV-2 spread so effectively when the original SARS fizzled out? Much of the answer lies in subtle differences in the spike protein, which we can analyze computationally to understand viral infectivity.
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White blood cell smear Module 4
Training a Computer to Classify White Blood Cells
Apply classical machine learning to a real diagnostic challenge: segment microscopy images, extract morphological features, and classify white blood cells into clinically relevant categories.
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Phillip Compeau

Each module in Biological Modeling is built around a real question in computational biology, and we use real tools to solve it. Bringing this work to the world with a student team has been one of the great joys of my career.

Phillip Compeau Founder of Biological Modeling
Professor at Carnegie Mellon University
A Philomath Course

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