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Biological Computation 20.181 Homework 10 Note: If your grade on this assignment increases your HW average then it will be weighted as two assignments, otherwise it will be weighted as a single assignment. Part 1. Accompanying this assignment is some python code that implements Dan Gille- sipie’s “Direct Method” for computing the exact behavior of discrete chemical systems (gillespie.py). Modify the code so that it implements Dan’s “First Reaction Method.” See some potentially useful hints at the end of the assignment if you want. Part 2. You should now have two discrete reaction event simulators. Use each simulator to compute the behavior of the system specified by the provided input files (system1.inp, species1.inp) over a period of 100 seconds, sampling the system state every 0.1 seconds. Report how long it takes each simulator to run and whether or not this time agrees with your expectation of the computational costs of each algorithm. Part 3.
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This note was uploaded on 11/11/2011 for the course BIO 20.010j taught by Professor Lindagriffith during the Spring '06 term at MIT.
- Spring '06