High throughput genomic technologies are leading to the generation of vast amounts of data on cellular components, detailing their expression, interactions and organization within biochemical pathways. To understand how these relationships result in a functional pathway, a variety of computational tools have been proposed that attempt to simulate the behavior of the molecular components. In general, these tools tend to neglect the spatial organization of molecules, typically treating the system of interest as a homogenous mix of components. However, there is increasing evidence that factors such as the co-localization of components have the potential to significantly influence pathway function and efficiency.

To account for these spatial factors we have created Cell++, a novel spatio-temporal modeling platform that performs three-dimensional simulations of biochemical pathways. Combining a cellular automata engine with Brownian dynamics, Cell++ is capable of simulating the bulk properties of large quantities of small molecules (e.g. calcium ions, pyruvate, ATP), while simultaneously allowing larger molecules such as enzymes to be treated as more complex entities. Cell++ is a current sourceforge project that is made freely available under the GNU general license. If you are interested in contributing to the project please contact us.

We are applying Cell++ to the study the impact of spatial organization on several biochemical systems including metabolism, signaling pathways, calcium waves and lipid raft mediated signalling.