Simulation of Biological Systems using Dynetica

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

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Substances

• Protein monomers, P
• Protein dimers, P2

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Reactions

• P P P2 (dimerization)
• P2 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/progre
  ssive
• Doesnt appear to handle vectors and matrices
• Needs correct version of java installed