simulation of biological systems using dynetica. dynetica is a simulation tool it can be downloaded...
Post on 19-Dec-2015
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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