Stochastic Simulations with StochKit2
StochKit2 provides command‐line executables for running stochastic simulations using variants of Gillespie’s Stochastic Simulation Algorithm and Tau‐leaping.
- Install Visual Studio: Download Visual Studio Community (free download link).
- Download StochKit2 form sourceforge and save it to the installation folder.
- Open the StochKit2<version>_WINDOWS folder
- Double click ‘StochKit.sln’ or right click the icon and open with Visual Studio , which will load Stoch Kit into Visual Studio. Visual Studio will convert the Stoch Kit project to your version. After the project is converted, close Visual Studio.
- Open Mixed_Compiled_Solution\Mixed_Compiled_Solution.sln in Visual Studio by double‐clicking to convert to your Visual Studio version. After the project is converted, close Visual Studio.
- Open the Visual Studio Command Prompt (Start ‐> All Programs ‐> Microsoft Visual Studio 2010 Express ‐> Visual Studio Command Prompt (2010)).
- Run Installation.bat (you can just drag the file into the Visual Studio Command Prompt and click enter or ‘cd’ to the Stoch Kit directory and type ‘Installation.bat’ and enter).
- Wait while StochKit is installed.
Creating a Model
You can use Sencillo a Python version of Facile to create an .xml model-file from a text-file.
- Create a .eqn (equation) file with a text editor and save it to you Stochkit folder (e.g. C:\StochSim\Model.eqn). The file should contain the parameters, reactions and initial conditions of your model for example;
- Make sure you installed Python and added the Python-folder to your system path (Windows: go to explorer: control panel > system and security > system; click advanced settings; click "environmental variables"; scroll to variable "Path" and add your sencillo folder path to the "value" area after a semicolon e.g. ...;C:\Python27\). This allows you to use Python commands in the windows terminal.
- Download Sencillo [here] and save it to the same folder as Stochkit (e.g. C:\StochSim). Navigate to the folder using the terminal.
- Simply run the command:
- Use Model.xml as input for Stochkit
parameter kon = 28.82326214225031 parameter koff = 15.9527830278967 parameter v = 250.6026048853528 parameter d = 1 parameter prod = 2 parameter deg = 1 D_off -> D_on; kon D_on -> D_off; koff D_on -> D_on + M; v M -> null; d M -> M + P; prod P -> null; deg D_off = 1 D_on = 0 M = 2 P=0
sencillo.py -s Model.eqn
to generate the Model.xml file (it will be saved as C:\StochSim\Model.xml)
Run Gillespie Simulation
- Open the Visual Studio terminal and navigate to your Stochkit folder
- run the command:
.\ssa -m models\examples\dimer_decay.xml -t 10 -r 100 -i 10 --keep-trajectories -f
- "-m directory" tells the driver where in the Stochkit folder your xml-model is
- "-r 100" means 10 0 realizations of the model are computed
- "-t 10" means the whole simulation time will be split into 10 time intervals.
- Optional inputs:
- "-i 5" indicates that data should be kept at 5 evenly‐spaced time intervals. In this example, data will be stored at time points 0, 2, 4, 6, 8, and 10. NOTE: data is stored at 6 time points when the number of intervals is 5. When 0 is chosen, data is kept only at the end time.
- "--keep-trajectories" tells the driver to keep trajectory data. This will create an output directory named <output directory>/trajectories that will contain one file for each realization. Use this option with caution since running a large number of realizations and keeping data at a large number of intervals will lead to StochKit producing a large amount of output data.
- "-f" short for "--force" specifies that we want to overwrite the existing output directory with our new data. If we had omitted this option, we would have received an error message.
keep in mind that for Windows you need to use backward slash "\" in the terminal, while for linux and mac you work woth forwardslash "/"