Ever since the first version of URDME, a software framework based on our theoretical work on RDME simulations on unstructured meshes, was made public in 2008, we have wanted to write up a journal publication that describes the software. For variuos reasons we have not gotten around to it, until now.
The paper, published in BMC systems Biology, contains two modeling examples and one example that illustrates how one can use the framework as a tool in methods development. We also discuss the relationship between URDME and two other great RDME simulators, mesoRD and STEPS.