Data and Resource Center
SPARC4 supports the creation of a multifunctional online hub facilitating coordination, synthesis, and prediction via three Core functionalities:
- Data Coordination Core [DAT-CORE] – Store, organize, manage, and track access to data and resources generated by SPARC.
- Map Synthesis Core [MAP-CORE] – Build interactive, modular, continually updated visualizations of nerve-organ anatomy and function.
- Modeling and Simulation Core [SIM-CORE] – Develop an online framework capable of hosting and connecting simulations to create predictive, multiscale, multiphysics models spanning from modulation sources acting from feasible access points to organ functional responses.
The Data and Resource Center (DRC) will host an interactive atlas of human and selected animal peripheral nervous systems, spanning from the end organs under study in SPARC to potential neuromodulation intervention points. Atlas users will be able to design and place nerve stimuli and observe predictions of their end effects at multiple organs, while accounting for user-defined anatomical and physiological parameters. The system will be able to offer a readout of which input uncertainties drive the output uncertainty, providing guidance for where repeated measurements and new experiments are needed.
Funded investigators closely coordinate with the DRC to achieve the following:
- Integrate data to generate detailed, predictive, functional and anatomical neural circuit maps for major organs and their functionally-associated structures;
- Develop techniques and evidence-based approaches that will allow the research community to interactively access these maps;
- Develop therapeutic approaches for disease conditions.
Other activities will include but are not limited to: development of informatics tools, development of ontology and provenance tools, development of standards, curation of data, development or adaptation of common data elements, maintenance of documentation and protocols regarding tools and technologies developed by or brought into the SPARC program, promoting and facilitating data upload and release, and providing a mechanism to protect patient rights and data.
Currently and previously funded research:
Specific objectives for Data Coordination, Map Synthesis, and Simulation projects differ based on the respective funding opportunities listed below. These DRC projects, examples also listed below, are available for partnering and collaborating activities within and outside the SPARC consortium.
- (RFA-RM-16-008) Three projects funded through 5-year, OT3 Awards
- BLACKFYNN: A SCALABLE AND SUSTAINABLE PLATFORM FOR SCIENTIFIC DATA INTEGRATION AND ANALYSIS: The Blackfynn platform provides a single seamless point of data access and management for multi-modal data. It enables rapid viewing and searching, integration and linking of data across modalities, and analysis via custom or standardized tools. There are three main goals for this project: the first is to develop a cloud-based scientific data management platform tailored to the needs of SPARC investigators; the second is to drive collaborative efforts with the other SPARC cores and investigators and promote interoperability and seamless integration of systems; and the third is to develop a sustainable ecosystem for the neuroscience community outside and beyond the SPARC initiative.
- MULTI-SCALE, MULTI-ORGAN, MULTI-SPECIES SPARC MAP MANAGEMENT: This project will provide tools for visualizing autonomic nervous system data and models generated by the SPARC consortium through the use of ApiNATOMY to provide annotations for biological context and a framework for implementing biophysical concepts such as conservation of mass and conservation of energy. The project will ensure that suitable community standards such as CellML, SBML, FieldML and SED-ML are used (and if necessary, further developed) for encoding and annotating the data, models and simulations to ensure reproducibility, and to help ensure that all data and models are appropriately annotated to make them findable and accessible by the community in the DAT-CORE database. A portal, based on web 2.0 and subsequent standards, will be developed that brings the anatomy and multiscale physiology of all organ systems into a single database-driven user interface. The user will be able to examine data and models at all scales and to generate predictive multiscale models (solved with the SIM-CORE tools) to answer specific questions associated with the autonomic control of the visceral organs.
- OPEN PLATFORM FOR ONLINE SIMULATIONS FOR STIMULATING PERIPHERAL ACTIVITY TO RELIEVE CONDITIONS: It will be the central hub for hosting and connecting simulations across the whole SPARC community, with an eventual goal of opening it up to the neuroscience community. One of the core elements of the platform is a set of novel neuro- and physiology-functionalized human and animal anatomical models. 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.
No publications at this time.
This page last reviewed on January 8, 2020