ArticleFrontiers in neuroinformatics2022
Large-scale biophysically detailed model of somatosensory thalamocortical circuits in NetPyNE.
Article in Frontiers in neuroinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Computational investigation of circuit mechanisms underlying short-latency responses to cortical stimulation.bioRxiv : the preprint server for biology · 2026Article
- Data-driven mouse motor thalamus model reveals topography and spatial weight scaling govern spindle dynamics.Communications biology · 2026Article
- Uncovering putative neural mechanisms of neurotherapeutic impacts on EEG using the Human Neocortical Neurosolver.bioRxiv : the preprint server for biology · 2026Article
- Pathway-Specific Ultrastructure of Thalamocortical Synapses in Mouse Somatosensory Area S2.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2025Article
- Closed-Loop Connectivity Best Supports Angular Tuning and Sleep Dynamics in a Biophysical Thalamocortical Circuit Model.bioRxiv : the preprint server for biology · 2025Article
- On the validity of electric brain signal predictions based on population firing rates.PLoS computational biology · 2025Article
- Circuits and mechanisms for TMS-induced corticospinal waves: Connecting sensitivity analysis to the network graph.PLoS computational biology · 2024Article
- Beyond Barrels: Diverse Thalamocortical Projection Motifs in the Mouse Ventral Posterior Complex.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2024Article
- Large-Scale Mechanistic Models of Brain Circuits with Biophysically and Morphologically Detailed Neurons.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2024Review
- A layered microcircuit model of somatosensory cortex with three interneuron types and cell-type-specific short-term plasticity.Cerebral cortex (New York, N.Y. : 1991) · 2024Article
- Methods and considerations for estimating parameters in biophysically detailed neural models with simulation based inference.PLoS computational biology · 2024Article
- The Roles of Potassium and Calcium Currents in the Bistable Firing Transition.Brain sciences · 2023Article
- The Role of Potassium and Calcium Currents in the Bistable Firing Transition.bioRxiv : the preprint server for biology · 2023Article
- Simulations of cortical networks using spatially extended conductance-based neuronal models.The Journal of physiology · 2023Review
- Multiscale model of primary motor cortex circuits predicts in vivo cell-type-specific, behavioral state-dependent dynamics.Cell reports · 2023Article
- Article
- Methods and considerations for estimating parameters in biophysically detailed neural models with simulation based inference.bioRxiv : the preprint server for biology · 2023Article
- Thalamic control of sensory processing and spindles in a biophysical somatosensory thalamoreticular circuit model of wakefulness and sleep.Cell reports · 2023Article
- Cortico-thalamic development and disease: From cells, to circuits, to schizophrenia.Frontiers in neuroanatomy · 2023Review
- Modernizing the NEURON Simulator for Sustainability, Portability, and Performance.Frontiers in neuroinformatics · 2022Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
The primary somatosensory cortex (S1) of mammals is critically important in the perception of touch and related sensorimotor behaviors. In 2015, the Blue Brain Project (BBP) developed a groundbreaking rat S1 microcircuit simulation with over 31,000 neurons with 207 morpho-electrical neuron types, and 37 million synapses, incorporating anatomical and physiological information from a wide range of experimental studies. We have implemented this highly detailed and complex S1 model in NetPyNE, using the data available in the Neocortical Microcircuit Collaboration Portal. NetPyNE provides a Python high-level interface to NEURON and allows defining complicated multiscale models using an intuitive declarative standardized language. It also facilitates running parallel simulations, automates the optimization and exploration of parameters using supercomputers, and provides a wide range of built-in analysis functions. This will make the S1 model more accessible and simpler to scale, modify and extend in order to explore research questions or interconnect to other existing models. Despite some implementation differences, the NetPyNE model preserved the original cell morphologies, electrophysiological responses and spatial distribution for all 207 cell types; and the connectivity properties of all 1941 pathways, including synaptic dynamics and short-term plasticity (STP). The NetPyNE S1 simulations produced reasonable physiological firing rates and activity patterns across all populations. When STP was included, the network generated a 1 Hz oscillation comparable to the original model
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