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Stochastic modeling

Stochastic modeling. Walk through stochastic simulation script. Visualize master equation. Exact particular trajectories. Ensemble distributions. Master equations: Dynamics of population fractions. m (copies mRNA). 0 copies. D t. Time. 0.

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Stochastic modeling

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  1. Stochastic modeling Walk through stochastic simulation script Visualize master equation Exact particular trajectories Ensemble distributions

  2. Master equations: Dynamics of population fractions m (copies mRNA) 0copies Dt Time 0

  3. Master equations: Dynamics of population fractions m (copies mRNA) 0copies Dt 2Dt 0

  4. Master equations: Dynamics of population fractions m + 1 m m - 1 0copies Dt 2Dt t t + Dt 0

  5. Master equations: Dynamics of population fractions m + 1 m m - 1 0copies Dt 2Dt t t + Dt 0

  6. Master equations: Dynamics of population fractions m + 1 m m - 1 0copies Dt 2Dt t t + Dt 0

  7. Stochastic modeling Walk through stochastic simulation script Visualize master equation Exact particular trajectories Ensemble distributions

  8. Walk-through of stochastic simulation script Specify system chemistry Use current state vector to calculate time to next event Use current state vector to choose type of next event

  9. Walk-through of stochastic simulation script Specify system chemistry Use current state vector to calculate time to next event Use current state vector to choose type of next event

  10. Specifying system System variables: System processes:

  11. Specifying system System variables: System processes:

  12. Specifying system System variables: System processes:

  13. Specifying system System variables: System processes:

  14. Walk-through of stochastic simulation script Specify system chemistry Use current state vector to calculate time to next event Use current state vector to choose type of next event

  15. Calculate average firing rates for each independent channel System variables: System processes: a1 a2 a3 a4

  16. Adding time-rates for individual channels a1 a2 a3 a4 a0

  17. Reaction channel firings in a population a0 a0 a0 a0 a0

  18. Reaction channel firings in a population a0 a0 a0 a0 a0

  19. Reaction channel firings in a population a0 a0 a0 a0 a0

  20. Reaction channel firings in a population a0 a0 a0 a0 a0

  21. Reaction channel firings in a population a0 a0 a0 a0 a0

  22. Reaction channel firings in a population a0 a0 a0 a0 a0

  23. Reaction channel firings in a population Zoomed in time scale a0 a0 a0 a0 a0 a0 a0 a0 a0 Dice represent shorter time intervals than before

  24. Reaction channel firings in a population a0 a0 a0 a0 a0

  25. Draw duration from exponential distribution

  26. Draw duration from exponential distribution

  27. Draw duration from exponential distribution

  28. Draw duration from exponential distribution

  29. Draw duration from exponential distribution

  30. Draw duration from exponential distribution

  31. Draw duration from exponential distribution

  32. Draw duration from exponential distribution

  33. Draw duration until next event from exponential distribution 0 1

  34. Draw duration from exponential distribution 0 1

  35. Draw duration from exponential distribution 0 1

  36. Walk-through of stochastic simulation script Specify system chemistry Use current state vector to calculate time to next event Use current state vector to choose type of next event

  37. Choose which event to perform 1 a4 a3 0 a2 a1

  38. Walk-through of stochastic simulation script Specify system chemistry Use current state vector to calculate time to next event Use current state vector to choose type of next event

  39. Walk-through of stochastic simulation script Specify system chemistry Use current state vector to calculate time to next event Use current state vector to choose type of next event mRNA Protein t

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