U24NS124001

Advancing Bio-Realistic Modeling via the Brain Modeling Toolkit and Sonata Data Format

One of the major goals of the Brain Initiative is to distill complex, multi-modal data into predictive frameworks via theory/modeling. As the planning document "Brain 2025: A Scientific Vision" urges, "theory and modeling should be woven into successive stages of ongoing experiments, enabling bridges to be built from single cells to connectivity, population dynamics, and behavior." However, data-driven, bio-realistic modeling is not widely practiced, in part because the field needs software supporting such complex modeling and standards for model sharing and reproducibility.

The Allen Institute has developed two powerful tools addressing these needs. One is the Brain Modeling Toolkit (BMTK) – a software suite for model building and simulation at multiple levels of resolution, from networks of biophysically detailed neuronal models, to point-neuron networks, to population-statistics approaches. The other one is the Sonata (Scalable Open Network Architecture Template) data format, which provides computationally efficient solutions for storing and exchanging data describing all stages of the modeling workflow (e.g., structure of model networks, configuration of simulations, simulation outputs). These tools were developed in coordination with many initiatives, such as NEURON, NEST, Neurodata Without Borders, NeuroML, PyNN, NetPyNE, and the Human Brain Project. As a result, BMTK and Sonata enable many applications and have generated substantial interest, with many users already employing these tools.

Most recently, BMTK and Sonata were instrumental in integrating diverse data from the Allen Institute and from the literature into some of the most sophisticated and bio-realistic models of a brain region to date. We propose to build a comprehensive user support and dissemination platform for BMTK and Sonata and help integrate these tools into model building and simulation practices in the community. In addition, the Allen Institute team joins forces with a University of Illinois team that developed a widely used molecular visualization software VMD. By integrating this software with Sonata, we will leverage its powerful existing capabilities to offer a free, highly efficient visualization tool for neuroscience modeling. Together, these tools will facilitate free exchange and reproducibility of models and support sophisticated modeling work – especially in cases of large-scale biologically realistic models relying on systematic integration of experimental data – for novice and expert users alike.

These contributions will advance the Brain Initiative's priority areas of theory and data analysis and integrated approaches and will strongly facilitate fairness (findability, accessibility, interoperability, and reuse of digital assets) in neuroscience modeling.

Allen Institute

(1) TO SUPPORT EXTRAMURAL RESEARCH FUNDED BY THE NATIONAL INSTITUTE OF NEUROLOGICAL DISORDERS AND STROKE (NINDS) INCLUDING: BASIC RESEARCH THAT EXPLORES THE FUNDAMENTAL STRUCTURE AND FUNCTION OF THE BRAIN AND THE NERVOUS SYSTEM; RESEARCH TO UNDERSTAND THE CAUSES AND ORIGINS OF PATHOLOGICAL CONDITIONS OF THE NERVOUS SYSTEM WITH THE GOAL OF PREVENTING THESE DISORDERS; RESEARCH ON THE NATURAL COURSE OF NEUROLOGICAL DISORDERS; IMPROVED METHODS OF DISEASE PREVENTION; NEW METHODS OF DIAGNOSIS AND TREATMENT; DRUG DEVELOPMENT; DEVELOPMENT OF NEURAL DEVICES; CLINICAL TRIALS; AND RESEARCH TRAINING IN BASIC, TRANSLATIONAL AND CLINICAL NEUROSCIENCE. THE INSTITUTE IS THE LARGEST FUNDER OF BASIC NEUROSCIENCE IN THE US AND SUPPORTS RESEARCH ON TOPICS INCLUDING BUT NOT LIMITED TO: DEVELOPMENT OF THE NERVOUS SYSTEM, INCLUDING NEUROGENESIS AND PROGENITOR CELL BIOLOGY, SIGNAL TRANSDUCTION IN DEVELOPMENT AND PLASTICITY, AND PROGRAMMED CELL DEATH; SYNAPSE FORMATION, FUNCTION, AND PLASTICITY; LEARNING AND MEMORY; CHANNELS, TRANSPORTERS, AND PUMPS; CIRCUIT FORMATION AND MODULATION; BEHAVIORAL AND COGNITIVE NEUROSCIENCE; SENSORIMOTOR LEARNING, INTEGRATION AND EXECUTIVE FUNCTION; NEUROENDOCRINE SYSTEMS; SLEEP AND CIRCADIAN RHYTHMS; AND SENSORY AND MOTOR SYSTEMS. IN ADDITION, THE INSTITUTE SUPPORTS BASIC, TRANSLATIONAL AND CLINICAL STUDIES ON A NUMBER OF DISORDERS OF THE NERVOUS SYSTEM INCLUDING (BUT NOT LIMITED TO): STROKE; TRAUMATIC INJURY TO THE BRAIN, SPINAL CORD AND PERIPHERAL NERVOUS SYSTEM; NEURODEGENERATIVE DISORDERS; MOVEMENT DISORDERS; BRAIN TUMORS; CONVULSIVE DISORDERS; INFECTIOUS DISORDERS OF THE BRAIN AND NERVOUS SYSTEM; IMMUNE DISORDERS OF THE BRAIN AND NERVOUS SYSTEM, INCLUDING MULTIPLE SCLEROSIS; DISORDERS RELATED TO SLEEP; AND PAIN. PROGRAMMATIC AREAS, WHICH ARE PRIMARILY SUPPORTED BY THE DIVISION OF NEUROSCIENCE, ARE ALSO SUPPORTED BY THE DIVISION OF EXTRAMURAL ACTIVITIES, THE DIVISION OF TRANSLATIONAL RESEARCH, THE DIVISION OF CLINICAL RESEARCH, THE OFFICE OF TRAINING AND WORKFORCE DEVELOPMENT, THE OFFICE OF PROGRAMS TO ENHANCE THE NEUROSCIENCE WORKFORCE, AND THE OFFICE OF INTERNATIONAL ACTIVITIES. (2) TO EXPAND AND IMPROVE THE SMALL BUSINESS INNOVATION RESEARCH (SBIR) PROGRAM; TO INCREASE PRIVATE SECTOR COMMERCIALIZATION OF INNOVATIONS DERIVED FROM FEDERAL RESEARCH AND DEVELOPMENT; TO INCREASE SMALL BUSINESS PARTICIPATION IN FEDERAL RESEARCH AND DEVELOPMENT; AND TO FOSTER AND ENCOURAGE PARTICIPATION OF SOCIALLY AND ECONOMICALLY DISADVANTAGED SMALL BUSINESS CONCERNS AND WOMEN-OWNED SMALL BUSINESS CONCERNS IN TECHNOLOGICAL INNOVATION. TO UTILIZE THE SMALL BUSINESS TECHNOLOGY TRANSFER (STTR) PROGRAM; TO STIMULATE AND FOSTER SCIENTIFIC AND TECHNOLOGICAL INNOVATION THROUGH COOPERATIVE RESEARCH AND DEVELOPMENT CARRIED OUT BETWEEN SMALL BUSINESS CONCERNS AND RESEARCH INSTITUTIONS; TO FOSTER TECHNOLOGY TRANSFER BETWEEN SMALL BUSINESS CONCERNS AND RESEARCH INSTITUTIONS; TO INCREASE PRIVATE SECTOR COMMERCIALIZATION OF INNOVATIONS DERIVED FROM FEDERAL RESEARCH AND DEVELOPMENT; AND TO FOSTER AND ENCOURAGE PARTICIPATION OF SOCIALLY AND ECONOMICALLY DISADVANTAGED SMALL BUSINESS CONCERNS AND WOMEN-OWNED SMALL BUSINESS CONCERNS IN TECHNOLOGICAL INNOVATION.

93.242 - Mental Health Research Grants

National Institute of Neurological Disorders and Stroke (NNDS) [HHS - NIH]

National Institute of Mental Health (NIMH) [HHS - NIH]

Seattle, Washington 981094307 United States

Single Zip Code

BRAIN Initiative: Research Resource Grants for Technology Integration and Dissemination (U24 Clinical Trial Not Allowed) (RFA-NS-19-006)

Amendment Since initial award the End Date has been extended from 08/31/26 to 02/28/27 and the total obligations have increased 2957% from $112,419 to $3,436,330.