The Simmune Analyzer is a tool that performs simulations assuming a well- stirred cell using models of cellular signaling networks defined with the Simmune Modeler. Different models with initial conditions and virtual experiments can be combined into simulation setups. All experiments assume a well- stirred cell. Cells can be stimulated with an extracellular ligand at user-specified times that can be removed from the simulation by adding a stimulus with 0 concentration. To perform more complex simulations with spatial resolution the ‘Simulator2’ should be used.

The general work-flow is to import one or more models from the Simmune Modeler using the Modeler Tab, then define one or more initial states for each of the imported models, next define a protocol specifying the duration of the simulation and optional stimuli. Then, an initial condition for a model is combined with a protocol and an optional variation of rate constants to define a simulation setup. Once created, the simulations will be started and results can be inspected by creating plots.

The Simmune Analyzer uses the open source database mongodb) to store its data. If a database server is set up in your lab you can connect to this server. When you connect for the first time, you'll be prompted for your user name and password. For details on the installation process refer to Section 13, “Administration of user accounts.” or Section 14, “Running Simmune on a cluster”. If you just want to run the Analyzer on your own computer, you'll have to download and install mongodb, when you start it for the first time. Simply select the File->Use Local Database option and follow the setup wizard that will guide you through the installation.