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Last updated:

December 7, 2022


Unlimited Duration


This course includes:

Unlimited Duration

Badge on Completion

Certificate of completion

Unlimited Duration


This course covers the analytical, graphical, and numerical methods supporting the analysis and design of integrated biological systems

Topics include modularity and abstraction in biological systems, mathematical encoding of detailed physical problems, numerical methods for solving the dynamics of continuous and discrete chemical systems, statistics and probability in dynamic systems, applied local and global optimization, simple feedback and control analysis, statistics and probability in pattern recognition.

An official course Web site and Wiki is maintained on OpenWetWare: 20.181 Computation for Biological Engineers.

Course Curriculum

    • Course Overview Unlimited
    • Review of UPGMA; Purpose of Phylogenetics; Newick Notation Unlimited
    • Python®: Trees; Data Structure, Parsing Function Unlimited
    • Parsimony; Sankoff Downpass Algorithm Unlimited
    • Downpass (cont.); Fitch’s Up Pass Unlimited
    • Up Pass (cont.) Unlimited
    • Parsimony (cont.); Unlimited
    • Greedy Algorithm for Trying Trees Unlimited
    • Introduction to The Protein Design Problem. What Makes Proteins Fold? Entropy Unlimited
    • Dihedrals, Build Order Unlimited
    • When to Use Computational Methods vs. Exact Methods Unlimited
    • Physics Model Underlying Exact Methods (cont.); Using Physics Model to Compute When a Reaction will Take Place. Unlimited
    • Review of How Physics Model Leads to Computational Method; Unlimited
    • Difference Between Reaction Rate and Reaction Propensity; Achieving Faster Computation Unlimited
    • Next Reaction Method Algorithm; Application to Genetic Memory (Latch) Unlimited
    • Review of Key Concepts Unlimited

About the instructor

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Massachusetts Institute of Technology