Skip to content

Adaptive Simplification of StochastIc SystEm with Reversible binding

Notifications You must be signed in to change notification settings

Mathbiomed/ASSISTER

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

9 Commits
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

ASSISTER (Adaptive Simplification of StochastIc SystEm with Reversible binding)

This is a matlab code for efficient and accurate simulations of stochastic biochemical systems containing rapid reversible binding reactions. Detailed step-by-step manual will be uploaded soon.

Code Description

  1. Gillespie_Reduction.m

Main function for this package. This function performs accurate and efficient stochastic simulations of models containing rapid reversible bindings, with the adaptive choice between two exclusively valid non-elementary propensities, the stochastic total quasi-steady-state approximation (stQSSA), and the stochastic low-state quasi-steady-state approximation (slQSSA). The below two functions are the auxiliary functions for this main function.

  1. QSSA_Threshold.m

This function determines which of the stQSSA and the slQSSA is valid and calculates the number of needed states (L) for the slQSSA to ensure the smaller error than the tolerance (epsilon) for given Kd value.

  1. LQSSA.m

This function calculates the L-state slQSSA of A in the reversible binding reaction (A + B <=> C) for given AT, BT, Kd, and L, where AT = A + C, BT = B + C, and Kd is the normalized dissociation constant (product of the system volume and the dissociation constant) of the reversible binding.

  1. test.m

This file contains an example code that runs the main function, Gillespie_Reduction.

  1. Codes_for_figs.zip

The matlab codes used for drawing figures in the manuscript and the supporting information.

About

Adaptive Simplification of StochastIc SystEm with Reversible binding

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages