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StochSS - An Integrated Development Environment for Simulation and Analysis of Biochemical Models.
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app Updated to 1.1 version of GillesPy Aug 10, 2017
conf Delete config Feb 11, 2016
examples Added Hes1 example Mar 3, 2016
jupyter_notebook_templates Fix for bug with parameter sweeps and species names Sep 15, 2016
jupyter_profile Launch a Jupyter notebook from the spatial results page Aug 10, 2016
pyurdme dn - Create StochSS Ami without extra steps for old ami layout Jan 28, 2015
release-tools deleting Mar 2, 2016
sdk/python Merge branch 'qsub' of into qsub_test Feb 14, 2017
stochss-launcher updated stochss.mac Feb 12, 2019
utils adding isolated jupyter notebook server for Aug 9, 2017
.gitignore visualize spatial jobs Feb 1, 2017
LICENSE LICENSE File added May 2, 2013 Update Jun 17, 2019
RELEASE_NOTES Release 1.9 Aug 10, 2017
StochKit2.0.11.tgz Include StochKit2.0.11 and PyURDME 1.0.1-stochss in the distribution … Feb 13, 2015
VERSION Release 1.9 Aug 10, 2017 now: asks for path to key pair before starting an inst… Feb 26, 2014 With a couple fixes verified to work with .apps on Mac Mar 17, 2014 clean up script; add no browser mode; fix up key exchange for previou… Feb 13, 2016
icon.tif Added icon Jul 11, 2013 Merge branch 'develop' into tutorial Mar 23, 2017
ode-1.0.4.tgz Updated ode-1.0.4 to fix linking issue Aug 29, 2016 fix for #648 Apr 24, 2017 Fixes for the embedded python package Jul 17, 2015 Updated ode-1.0.4 to fix linking issue Aug 29, 2016 refactor of the run scripts Aug 20, 2014 fixing install Aug 7, 2017
run_mac_install-embedded-python.scpt Fixes for the embedded python package Jul 17, 2015 Fixes for the embedded python package Jul 17, 2015
run_mac_install.scpt Changing the names from spatial to python for consistency Jun 6, 2015 adding python deps to run.mac Aug 24, 2016
stochoptim-0.5-1.tgz Updated stochoptim to test before using gsl-config Aug 26, 2014


StochSS - Stochastic Simulation Service.

StochSS is currently supported on Linux and Apple OSX platforms, and with preliminary support for Windows.

Obtaining StochSS:

The easiest and recommended way to obtain StochSS is to download the latest stable release and follow the install instructions at

This process uses the latest stable StochSS Docker image.

Launching StochSS from this repository

This uses the launcher tools from this repository. For the master branch, they are identical to the above provided stable releases. This process uses the latest stable StochSS Docker image.

  1. Clone the repository $ git clone --recursive

  2. Use 'stochss_launcher' to start the application

Installing and running from source (Advanced users only)

The will install and run StochSS as a native application on Linux or OSX. It requires installing all dependencies natively, which can be an error prone process. This mode is mostly recommended for developers seeking to modify StochSS.

The StochSS source is downloaded by cloning the GitHub repository. Since the repository relies on several submodules, a recursive cloning has to be performed. Open a terminal and from a directory to where you want to download the code, (your home folder is a good place) type the following command:

$ git clone --recursive

If git is not already installed on your machine, the above command will fail. To obtain Git for your platform:


$ apt-get install git


  • Install Xcode:
    • Xcode, Apples Integrated Development Environment, contains all the tools you need in order to install StochSS and StochKit2. Install Xcode for free from App Store.

    • After you have installed Xcode, you need to install the 'command line tools'. Open the Xcode application (in the "Applications" folder). Then, from the the Xcode menu: Xcode > Preferences > Downloads > Command Line Tools

Quick start:

In the stochss folder, type OSX:

$ ./


$ ./

If the webserver launched without error, the above scripts will open the App using your default webbrowser. You will be prompted to create an administrator account and from there can log in and use StochSS.

Terminating the App

Closing the browser does not terminate the App. If you used the Docker based package on OSX you will need to cancel the process in the StochSS window that launched when you clicked the App icon. On Linux, or if using the native version on OSX, you need to shut press Ctrl-C in the same terminal where you lunched the app. Please wait for jobs to finish or stop them before shutting the application down to avoid runaway background processes.

Building your own Docker images

The process described here will help you build your own local Docker images from any branch. This can be useful to create your own packages from e.g. the unstable devlop branch (where new features are pushed prior to release)

Deploying StochSS as a Service

The saas branch is used at to deploy as SaaS. It has a modified user authentication system based on email verification. The MOLNs software can be used to automate the deployment of StochSS in OpenStack clouds and in Amazon EC2.

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