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605.752 Simulation of Biological and Complex Systems

This course applies modeling and simulation to biological problems. To date, biological sciences have been extremely reductionistic, generating an enormous amount of disparate descriptive knowledge. A need is emerging to explore the integration of how these "parts" fit together through the use of new computational tools. The course begins with an overview of simulation techniques (e.g., cellular automata, differential equations models, Monte Carlo, and event-driven). The first half of the course covers simulation tools for modeling cells including Neuron, Gepasi, E-Cell, Virtual Cell, BioSpice, Genomic Object Net, Systems Biology Workbench, and the emerging SBML standard. The second half of the course covers simulation of multicellular phenomena using techniques from the field of complex systems using packages such as SWARM. Applications will be drawn from neuron modeling, cellular metabolism, genetic networks, whole cell models, and physiological models. Students will complete several simulation labs and a course project.

Prerequisites: Courses in molecular biology (605.205 or 410.602), differential equations, and probability.