Commit 8307551d authored by Urban BEZELJAK's avatar Urban BEZELJAK


parent c3c42f25
# Rab5 spatial stochastic model
This repository hosts the Rab5 activation stochastic model development, which supports the Loose and Saunders lab project with tentative title
**"Stochastic nucleation events trigger collective Rab GTPase activation"**.
The basic model was implemented with [Smoldyn]( stochastic simulator.
......@@ -66,3 +67,18 @@ Smoldyn uses parameters in micrometer and second units, which have to be recalcu
* continous membrane (periodic walls): [200330_Rab5config_nobounds.txt](200330_Rab5config_nobounds.txt)
### Python script for parameter scans
An example of Python script to run muntiple simulations with different GEF numbers:
import os
from subprocess import call
import time
filepath = input("Enter filepath (e.g. L:\Modeling\200325_Rab5config.txt): ")
for gefnum in [10,20,40,60,80,120,160,200,400]:
dir = r"C:\Program Files\Smoldyn"
cmdline = r"smoldyn %s --define GEFnum=%i -tqw" %(filepath,gefnum) #insert config file path
rc = call("start cmd /K " + cmdline, cwd=dir, shell=True)
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