Algebraic biology
Algebraic biology
Abram Gannibal Project
AIMS South Africa class (March-April 2020)
Books
- Mathematical Concepts and Methods in Modern Biology: using modern discrete models, edited by Raina Robeva and Terrell Hodge. Academic Press, 2013. Freely available with ScienceDirect subscription.
- Algebraic and Discrete Mathematical Methods for Modern Biology, edited by Raina Robeva. Academic Press, 2015. Freely available with ScienceDirect subscription.
- Algebraic and Combinatorial Computational Biology, edited by Raina Robeva and Matthew Macauley. Academic Press, 2018. Freely available with ScienceDirect, subscription.
- Probabilistic Boolean Networks: The Modeling and Control of Gene Regulatory Networks, by Ilya Shmulevich and Edward R. Dougherty. SIAM, 2010.
- Biological Feedback, by René Thomas and Thomas D'Ari. CRC Press, 1990 (updated 2006).
- Ideals, Varieties, and Algorithms: An Introduction to Computational Algebraic Geometry and Commutative Algebra, by David A. Cox, John Little, and Donal O'Shea. Spring, 2015 (4th edition).
Software
- TURING:
Algorithms for Computational with Finite Dynamical Systems. List of algorithms on AlgoRun.
- Sage: free open-source mathematics software. Can be downloaded or run online.
- Singular:
free open-source computer algebra system for polynomial computations, with special emphasis on commutative and non-commutative algebra, algebraic geometry, and singularity theory. Can be downloaded or run online.
- Macaulay2: free open-source software for computational algebraic geometry and commutative algebra. Can be downloaded or run online.
- The gfan package for computing the Gröbner fan of an ideal in Singular.
- GINsim (Gene Interaction Network simulation), a computer tool for modeling and simulation of Boolean and logical networks.
Code
Lecture notes
- What is Algebraic Biology? 13 pages. Updated Mar 18, 2020.
- Modeling the lac operon in E. coli. 43 pages. Updated Mar 19, 2020. Worksheet.
- Algebraic models and finite dynamical systems. 23 pages. Updated Mar 31, 2020. Worksheet.
- Chemical reaction networks. 12 pages. Updated Mar 31, 2020. Worksheet.
- Bistability in ODE and algebraic models. 28 pages. Updated Mar 31, 2020. Worksheet
- Dilution, degradation, and time delays in algebraic models. 18 pages. Updated Mar 31, 2020. Worksheet.
- Reduction of algebraic models. 16 pages. Updated Mar 31, 2020. Worksheet
- Reverse engineering the wiring diagram. 39 pages. Updated Apr 7, 2018.
- Reverse engineering the model space. 29 pages. Updated Apr 5, 2018. Worksheet
Important
Papers
Homework
- Homework 1: pdf | tex. Due Tuesday, March 24, 2020.
- Homework 2: pdf | tex. Due Tuesday, March 31, 2020.
- Homework 3: pdf | tex. Due Monday, April 6, 2020.