Method section of the Biophysical Journal Paper - "The maximum solubility product marks the threshold for condensation of multivalent biomolecules".
We perform stochastic rule based simulations using two solvers - SpringSaLaD and NFsim. We perform multiple stochastic trials and analyze them to get average properties of the system.
- We define the springsalad model using the in-built graphical interface and then launch multiple simulations using the batch file called "submit_ssalad.sh". The data analysis part is summarized by "ssalad_analysis.ipynb" inside the springsalad folder.
- We define the NFsim model using the Virtual Cell graphical interface and then launch multiple simulations using the batch file called "submit_nfsim.sh". The data analysis part is summarized by "NFsim_analysis.ipynb" inside the NFsim folder.
To use the code, simply clone the repository to your local machine.