This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Our group develops computational and experimental methods to estimate the parameters of gene network models. These models are generalization of chemical kinetics models. They can either represented by differential equations or by stochastic processes. We use optimization algorithms to fit gene network models to experimental data. The size of the parameter space of our models along with their nonlinearity can make them difficult to optimize. In situation where we have to use stochastic models to simulate the biological system that we have characterized experimentally, the computational cost of optimizing the model is even greater. Depending on the models and parameters used, a typical optimization problem can require 100s of CPU hours. In addition to getting us access to a HPC environment for our own use, I want to better understand the resources available through the TeraGrid that could be used to help bring the benefit of HPC to my scientific community. This is especially important because very few people in my field have the expertise to work in a HPC environment even though many people could benefit from it. The attached manuscript describes an application that we are about to release in which we have addressed this need by providing users with a build-in access to a cluster. Users run the application on their desktop and can elect to execute simulations on a remote machine. We have implemented this mechanism on a 8 node dedicated cluster as proof of concept but this solution is not scalable. We would like to see to what extent we could provide people in our community easy access to the TeraGrid through the development of specific client-server applications to analyze gene networks. Once we have a better understanding of the TeraGrid environment, I will submit a separate request for advanced support to analyze with the TeraGrid staff the possibility to develop a specific gateway. I dont have a specific grant associated with that request at this point. However, I need to be able to articulate how the TeraGrid fits in the research plans of many of several grants that I am currently preparing for the NIH and NSF.
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