MATSim provides a toolbox to run and implement large-scale agent-based transport simulations. The toolbox consists of several modules which can be combined or used stand-alone. Modules can be replaced by own implementations to test single aspects of your own work. Currently, MATSim offers a toolbox for demand-modeling, agent-based mobility-simulation (traffic flow simulation), re-planning, a controller to iteratively run simulations as well as methods to analyze the output generated by the modules.
For more information, see the project website at http://www.matsim.org/.
The issue tracker is at http://matsim.atlassian.net/.