bio-physics-wiki

StochKit2  provides  command‐line  executables  for  running  stochastic  simulations 
using  variants  of  Gillespie’s  Stochastic  Simulation  Algorithm  and  Tau‐leaping.  


== Installing Stochkit ==
(for Windows)
# Install Visual Studio: Download Visual Studio Community (free download [http://go.microsoft.com/fwlink/?LinkId=517284 link]).
# Download StochKit2 form [http://sourceforge.net/projects/stochkit/ sourceforge] and save it to the installation folder.
# Convert  StochKit  to  match  your  version  of  Visual Studio 
## 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. 
# Build StochKit 
## 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. 
(for MacOS)
# Download StochKit2 form [http://sourceforge.net/projects/stochkit/ sourceforge] and save it to the installation folder.
# cd to the installation folder and execute install.sh
# Add stochkit to your system path. In the termianal type: 
 sudo nano /etc/paths
        add the location of the installation folder and the /bin subdirectory to the directory list
# you can use the terminal to execute ./ssa commands (no need for visual studio)

== Creating a Model ==
You can use Sencillo a Python version of Facile to create an .xml model-file from a text-file. 

<ol>
<li> 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;</li>
 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
<li> 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.</li>
<li> Download Sencillo [[http://swainlab.bio.ed.ac.uk/software/sencillo/ here]] and save it to the same folder as Stochkit (e.g. C:\StochSim). Navigate to the folder using the terminal. </li>
<li> Simply run the command: </li>
 sencillo.py -s Model.eqn
to generate the Model.xml file (it will be saved as C:\StochSim\Model.xml)
<li> Use Model.xml as input for Stochkit </li>
</ol>

== Run Gillespie Simulation ==
<ol>
<li> Open the Visual Studio terminal and navigate to your Stochkit folder </li>
<li> run the command: </li>
 .\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 "/"
 </ol>