Summary/Abstract for NIH-SPARC SIM-CORE
The goal of the project is to establish a comprehensive, intuitive, freely accessible online platform for the SPARC program to use to simulate and study in a precise and predictive manner nerve electrophysiology and its interaction with organ physiology. The platform, which forms one of the three integrative cores of the SPARC Data Resource Center, will be the central hub for hosting and connecting simulations across the whole SPARC community. The use of state-of-the art functionalized anatomical models will make it possible to perform simulations ranging from the molecular scale up to the complexity of the human body.
The platform will eventually be opened to the entire neuroscience community to provide users with an interactive approach to effectively develop, extend, validate, certify, document, store, share, and apply models, explore the impact of stimulation parameters, and create predictive, multi-scale, multi- physics models for a wide range of scenarios. It is composed of a powerful, web-based graphical user interface (GUI), a cloud computing platform, flexible coupling and analysis frameworks, image segmentation tools, a Python scripting interface, and a range of flexibly deployable services (e.g., electromagnetic and electrophysiology solvers). One of the core elements of the platform is a set of novel neuro- and physiology-functionalized human and animal anatomical models (NEUROCOUPLE and NEUROFAUNA, respectively). The models will allow simulation of in vivo fields generated by implanted or external stimulators, elucidation of the resulting neuromodulations, and assessment of the changes induced in organ physiology.
With the web-based GUI and the Python scripting interface, the user can (i) connect existing and/or novel computational models to perform studies, (ii) easily integrate new structures (e.g., nerve microstructure) into the anatomical models, and (iii) generate new computational services, simulation studies, and anatomical models that can be shared with other users/researchers according to project- specific requirements. Advanced analysis tools that allow, e.g., sensitivity and uncertainty evaluations or optimization-based parameter fitting to be performed will be made available, so that the models can be collaboratively investigated by researchers in- and outside the SPARC community.
By offering within the SPARC DRC a powerful and flexible simulation platform developed according to open-source philosophy, the goal is to create a sustainable, versatile environment that facilitates and encourages community-based model development and that leverages the individual advances of the SPARC teams to create a combined contribution greater than the sum of its parts.