Simulation of Biological Systems using Dynetica

• Dynetica is a simulation tool

• It can be downloaded for free from the web (http://www.duke.edu/~you/Dynetica_page.htm)

• Once it is downloaded, you can run it using the command window

Substances

• Protein monomers, P:

• Protein dimers, P2:

Reactions

• P + P P2 (dimerization)

• P2 P + P (dissociation)

Choice of Simulation Algorithms

• Runge-Kutta

• Variable time-step Runge-Kutta

• Gillespie Direct Method

• Optimized Direct Method

• Gillespie First Reaction Method

Deterministic simulation: Runge-Kutta

• Maximum timestep, e.g. 0.01 seconds

• Sampling timestep, e.g. 0.1 seconds

• Number of iterations, e.g. 1000.

Stochastic simulation: Gillespie Direct method

• Number of iterations, e.g. 1000

• Number of rounds, e.g. 1000

• Save output

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