Neuroinformatics tools for declarative multiscale modeling via automatic generation of implementations, applied to large-scale models of the vertebrate retina

• Grant number: 17/04748-0
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: October 01, 2017
• End date: April 30, 2018
• Field of knowledge: Engineering - Biomedical Engineering
• Principal Investigator: Antonio Carlos Roque da Silva Filho
• Grantee: Bóris Marin
• Host Institution: Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
• Associated research grant: 13/07699-0 - Research, Innovation and Dissemination Center for Neuromathematics - NeuroMat, AP.CEPID

Abstract

Novel experimental techniques have enabled mapping brain structure and function with unprecedented resolution and precision, across multiple scales: synapses, cells, up to neuronal population dynamics in freely behaving animals. Increasingly detailed computational models have been used to systematically investigate the role of low-level mechanisms - eg electrophysiology - in the emergence of higher-level phenomena, such as behaviour. The myriad of techniques and technologies involved in this approach - linked to the sheer volume of experimental data and associated analysis techniques - hamper new users from understanding, evaluating and reusing models developed within a different research group. We propose a set of measures whose core involves developing, improving and promoting the standardisation of models in computational biology. Through open standardised declarative descriptions, independent from implementation details (such as numerical methods, simulators or analysis libraries), operating at levels of abstraction closer to that of cellular neurophysiology, we hope to contribute towards greater accessibility - and consequent verifiability, reproducibility and reuse - of such models. This infrastructure also enables efficient simulation and data analysis through automated code generation, targeting novel architectures such as GPUs, FPGAs and neuromorphic hardware. (AU)

Scientific publications

(5)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

BLUNDELL, INGA; BRETTE, ROMAIN; CLELAND, THOMAS A.; CLOSE, THOMAS G.; COCA, DANIEL; DAVISON, ANDREW P.; DIAZ-PIER, SANDRA; MUSOLES, CARLOS FERNANDEZ; GLEESON, PADRAIG; GOODMAN, DAN F. M.; et al. Code Generation in Computational Neuroscience: A Review of Tools and Techniques. FRONTIERS IN NEUROINFORMATICS, v. 12, NOV 5 2018. (17/04748-0)

GLEESON, PADRAIG; CANTARELLI, MATTEO; MARIN, BORIS; QUINTANA, ADRIAN; EARNSHAW, MATT; SADEH, SADRA; PIASINI, EUGENIO; BIRGIOLAS, JUSTAS; CANNON, ROBERT C.; CAYCO-GAJIC, N. ALEX; et al. Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits. NEURON, v. 103, n. 3, p. 395+, AUG 7 2019. (17/04748-0)

DEPETRI, GABRIELA I.; PEREIRA, FELIPE A. C.; MARIN, BORIS; BAPTISTA, MURILO S.; SARTORELLI, J. C.. Dynamics of a parametrically excited simple pendulum. Chaos, v. 28, n. 3, MAR 2018. (11/19296-1, 14/07043-0, 17/04748-0)

CANTARELLI, MATTEO; MARIN, BORIS; QUINTANA, ADRIAN; EARNSHAW, MATT; COURT, ROBERT; GLEESON, PADRAIG; DURA-BERNAL, SALVADOR; SILVER, R. ANGUS; IDILI, GIOVANNI. Geppetto: a reusable modular open platform for exploring neuroscience data and models. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, v. 373, n. 1758, p. 13-pg., 2018-10-19. (17/04748-0)

CANTARELLI, MATTEO; MARIN, BORIS; QUINTANA, ADRIAN; EARNSHAW, MATT; COURT, ROBERT; GLEESON, PADRAIG; DURA-BERNAL, SALVADOR; SILVER, R. ANGUS; IDILI, GIOVANNI. Geppetto: a reusable modular open platform for exploring neuroscience data and models. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, v. 373, n. 1758, SI, OCT 19 2018. (17/04748-0)