Computer Methods for Physiological Problems

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Project Summary This project provides the core facility needed by the NEURON user community through management of development, maintenance, dissemination, and teaching. NEURON is an open source simulator for neurons and neural circuits that runs under OS X, MS Windows, and UNIX/Linux, on hardware ranging from laptops to massively parallel supercomputers. More than 1900 publications report work done with it. Many projects contribute to NEURON's capabilities, and many more depend on its continued development and support. Our development plan addresses challenges faced by NEURON users in working with experimentally-driven models of cells and networks, whose increasing complexity poses a growing computational burden. These models are well suited to large computer clusters, but much greater performance is achievable by exploiting the architecture of new hardware such as the NVIDIA GPU and the many core Intel PHI. Factoring out NEURON’s solver engine into a standalone CoreNEURON program cut memory use by an order of magnitude and makes it possible to focus on architecture-specific memory layout for optimal performance. This must now be transformed into a dynamically loadable library to allow the standard interpreter control required for interactive model development and simulation analysis. Increased model complexity also requires special measures to facilitate the construction, analysis, and reuse of empirically based computational models. We will extend NEURON’s ModelView tool to display subcellular model specifications described with NEURON’s model description language (NMODL). These specifications will also be used to generate equivalent model descriptions compliant with NeuroML’s Low Entropy Modeling System (LEMS) standard. These changes will allow entire cell model descriptions to be translated from NEURON to NeuroML, and enable full interoperability between NEURON and other NeuroML compatible simulators. Dissemination and support activities will include: software maintenance necessary to ensure that users continue to be able to run NEURON under all combinations of OS X, MS Windows, UNIX/Linux, and with any or no version of Python and MPI; active support of users through email and the NEURON Forum; creation of new documentation and publication of articles and reports; presenting courses and organizing meetings of NEURON users.