New paper published on Symmetry
One of the core topics of our research group is mechanistic biochemical modeling. The analysis of such models is often performed using simulations, which can be extreme from a computational point of view. Hence, we worked a lot on the acceleration of methods. In order to investigate the performances our algorithms, we need a large amount of arbitrarily complex and fully parameterized models to be simulated.
To this aim, we created SMGen, a new open source generator of biochemical reaction networks. SMGen gives the user the freedom to specify a lot of parameters: the number of chemical species, the number of reactions, the order of the reactions, wheher to use concentrations or molecules count, and so forth. SMGen can export the model in SBML format, so that it can be loaded and run in virtually every existing tool for systems biology.
You can read our paper on SMGen on Symmetry 14(1).