Title: Simmune - a biologist-friendly ‘computational microscope’ for modeling cellular signaling processes 

Speaker: Dr. Thorsten Prustel (Laboratory of Immune System Biology, NIH)

Abstract: Rapid advances in experimental techniques, such as high-resolution microscopy and proteomics, permit to characterize spatiotemporal distributions of proteins and other molecular components within cells in unprecedented detail. However, to correlate this wealth of detailed quantitative data with cellular physiology requires the capability to create and explore complex models that involve such large numbers of molecular components and interactions that would be prohibitively complicated to account for with traditional approaches to modeling the reaction dynamics. Another obstacle to the use of mechanistic models of cellular behavior is the frequently incomplete experimental knowledge of model parameters such as reaction rates. 
In my talk, I will describe how the simulation software Simmune addresses these challenges and can be used to generate predictive spatially-resolved models. Simmune provides a visual language for molecular states and bimolecular interactions that permits experimentalists without a computational background to create realistic models of cellular signaling pathways. A computational representation of the reaction network of all possible multi-molecular complexes is automatically generated and embedded into realistic models of cellular morphology. Furthermore, Simmune permits to perform broad range parameter variations to identify the parameters that strongly influence the signaling system's behavior. I will illustrate Simmune's capabilities with examples of G-protein coupled receptor signaling and crosstalk in common gamma chain signaling. 
This work was supported by the Intramural Research Program of the NIH, NIAID.