StochSS - Stochastic Simulation Service.

StochSS is currently supported on Linux and Apple OSX platforms.

StochSS 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 https://github.com/StochSS/stochss.git

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

Ubuntu/Debian:

$ apt-get install git

Fedora:

$ sudo yum install git-core

MacOSX:

• 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

The application makes use of StochKit2 to run well mixed stochastic simulations locally, and to use this feature you need to install StochKit2. StochSS contains a tool that will attempt to automatically download and install StochKit2.0.7 and configure the StochSS App to use this installation.

After sucessfully cloning the repository as above, in a terminal, type:

$ cd stochss
$ tools/install_stochkit.sh

You can expect the StochKit installation to take a few minutes to complete. If the script above fails, you need to consult the StochKit manual for troubleshooting the installation. On Ubuntu and Fedora, the script will try to install any dependencies (make, gcc, g++, libxml2) using the standard package managers. On MacOSX, since there are many different ways to satisfy the dependencies, we do not attempt an automatic install. If you have Xcode and the command-line tools installed as recommended above, all dependencies are satesfied.

If you only plan to run StochKit in virtual machines, you can skip the above steps.

In the stochss folder, type

$ python launchapp.py

If the webserver launched without error, the above script will open the App using your default webbrowser. The App will be served on the follwing address

http://localhost:8080

If you prefer to use another browser than the default, simply navigate to the above address.

You will be prompted with a login screen with the default username 'test@examples.com'. This version of StochSS does not support a secure authentication mechanism, so any user name that is on the form of an e-mail address will do to log in to the app. The e-mail you use will be mapped to a user id, so whenever logging in with the same e-mail address at a later time, your saved data will be available in the new session. With that said, since the app is in beta-status, we recommend that you save important models frequently by exporting them to StochKit's native XML format.

Closing the browser does not terminate the App. To shut it down permanently, in the same terminal where you lunched the app, press "Ctrl-C" on your keyboard, after which you can close the terminal. Note that the data created in the app is not persisted until the app is terminated. If the app is not terminated normally, the pending transactions will not be applied and the data will be lost.

To launch the app on a different host and port, from the base directory:

$ python sdk/python/dev_appserver.py --host hostname --port portnumber app

For more options, consult the help for dev_appserver.py.