The models consist of human immune response to tuberculosis in the lung, lymph node and brain, and a human breast cancer model. The models can be agent based models (ABM), ordinary differential equations (ODE) or partial differential equations (PDE). They can also be hybrid models, for example an ABM of the lung that interacts with an ODE of a lymph node. Whereas an equation based model represents and tracks aggregate model attributes, such as total number of activated macrophages, an ABM represents and tracks individual entities, for example each distinct activated macrophage. The ABM's are implemented in C++, using a variety of libraries as described in the details for each model. The ODE's and PDE's are typically implemented in Matlab or perhaps in R.
The following are useful references on modeling and the immune system.
See Model History for an overview of the history of the lab models and descriptions of legacy models no longer actively developed.
Each model description specifies the tool set it uses to build, run and process run results. Many (most) of these are used for several of the models. There are several choices for editing and debugging C++ source code. Qt Creator is typically used on Linux, Xcode on Macs and Visual Studio on Windows. Previously we used Eclipse, CDT and Subclipse on Linux, but Qt Creator has better C++ support, especially for debugging. We may switch to Qt Creator on Windows and/or Macs as well. You are welcome to use whatever editing, build and debugging tools you like, but we can best support the ones we are most familiar with.
The models use either the El Kebir framework or Vogt framework. Model run results are stored on the model run server.
include reference to LHS paper and to Sim's UA/SA paper. Describe LHS parameter files and LHS program.