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Simulation of Biological Systems using Dynetica
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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
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Substances Protein monomers, P: Protein dimers, P 2 :
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Reactions P + P P 2 (dimerization) P 2 P + P (dissociation)
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Choice of Simulation Algorithms Runge-Kutta Variable time-step Runge-Kutta Gillespie Direct Method Optimized Direct Method Gillespie First Reaction Method
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Deterministic simulation: Runge- Kutta Maximum timestep, e.g. 0.01 seconds Sampling timestep, e.g. 0.1 seconds Number of iterations, e.g. 1000.
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Stochastic simulation: Gillespie Direct method Number of iterations, e.g. 1000 Number of rounds, e.g. 1000 Save output
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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
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