Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part I: Anatomy and Part II: Physiology & Experimentation (eLife 2024)

Reimann et al. and Isbister et al. built and simulated a highly detailed computational model of the non-barrel primary somatosensory cortex of the juvenile rat. This biophysical model is available in SONATA format and is comprised of over 4 million neurons and 14 billion synapses.

Cortical cell assemblies and their underlying connectivity: An in silico study (PLOS 2024)

Ecker et al. developed an approach to identify functional cell assemblies and uncover the structure of synaptic connectivity that underlies the formation of such assemblies. They do so in a large-scale cortical network model available in SONATA format.

Spatially targeted inhibitory rhythms differentially affect neuronal integration (eLife 2024)

Headley et al. used a model of a L5 pyramidal neuron in BMTK to investigate how the differential spatial targeting and rhythmic frequency of inhibitory inputs onto pyramidal neurons impacts signal integration.

BMTK can now import electrophysiological experimental data from the DANDI Archive into models and simulations. With no programming required, users can filter DANDI datasets and individual unit recordings to be streamed during simulation time. See details in this example.

This hands-on workshop focuses on building and simulating complex and heterogeneous network models grounded in real biological data. Participants will learn to use BMTK, SONATA, VND, our data, and models for simulating brain circuits. The 2025 workshop will be held July 28th-30th, 2025 at the Allen Institute in Seattle, WA.

Applications are due March 15th, 2025! Selected applicants will be notified by May 1st, 2025. Limited travel funding available. See event page for full details.

Ito et al. use a stabilized supralinear network (SSN) model to investigate how cortical circuits adapt to stimulus novelty. By integrating structural and physiological data, the study suggests that novelty generally weakens cortical connections and shifts inhibitory neuron dynamics, particularly between SST and VIP populations. The SSN modeling framework used in this work will be soon incorporated into BMTK.

VND neuronal visualization software now offers cell morphology coloring by compartment type. In the illustration, axons are shown in green, basal dendrites in red, apical dendrites in blue, and cell somas in silver. Combined with selection and highlighting of individual cells and cell populations, the coloring method can be used to explore distribution and proximity of cell morphology compartments across a model neuronal system. Compartment-type coloring can be applied to all VND morphology drawing styles (line, draft morphology, and full-quality morphology).

Received this newsletter as a forward? Subscribe here for updates.

615 Westlake Ave N | Seattle, WA 98109 US