This site documents the software development infrastructure used by the Kirschner and Linderman labs to develop and maintain a variety of simulation models of human biological disease processes. It provides details on the software development and modeling tools used - where to get them, how to install them, how to use them. It also specifies what models are under development, what platforms they run on, what tool set is required for each model, etc. It is intended for use by researchers who need to use and develop the models and by staff programmers who assist the researchers in that task.
Given the scope of the work, the large amount of detail involved and the rapidly evolving nature of computer technology, this documentation is bound to contain mistakes and omissions. In particular, installation instructions for a version of a software tool for a version of an operating system may not be entirely valid (or valid at all) for a later version of the tool or operating system. Links to some outside web pages not under our control are bound to change or no longer be available. Please inform the IT staff of any problems encountered so that we can keep this site as current as possible.
Information on the models and software frameworks used to implement them can be found on the Models page.
Information on the various types of computer systems, including centralized compute resources (ex. clusters, etc.) can be found on the Systems page.
We use a variety of software tools to build and run the models and post-process the model results. See the main tools page for general information on the tools we use and information about specific tools, such as how to install and use them on specific operating systems.