1. Simulation of Biological Systems using Dynetica

2. Dynetica is a simulation tool It can be downloaded for free from the web (http://www.duke.edu/~you/Dynetica_page.htm)http://www.duke.edu/~you/Dynetica_page.htm Once it is downloaded, you can run it using the command window

4. Substances Protein monomers, P: Protein dimers, P 2 :

5. Reactions P + P P 2 (dimerization) P 2 P + P (dissociation)

10. Choice of Simulation Algorithms Runge-Kutta Variable time-step Runge-Kutta Gillespie Direct Method Optimized Direct Method Gillespie First Reaction Method

11. Deterministic simulation: Runge- Kutta Maximum timestep, e.g. 0.01 seconds Sampling timestep, e.g. 0.1 seconds Number of iterations, e.g. 1000.

13. Stochastic simulation: Gillespie Direct method Number of iterations, e.g. 1000 Number of rounds, e.g. 1000 Save output

20. Dynetica Summary Runs quickly, no bugs found so far Choice of deterministic and stochastic algorithms Can handle different types of kinetics, e.g. mass-action, michaelis-menten, equilibrated/progressive Doesn’t appear to handle vectors and matrices Needs correct version of java installed