[Comp-neuro] Modeling milestones from the Allen Institute for Brain Science

Anton Arkhipov antona at alleninstitute.org
Mon Dec 3 07:49:15 CET 2018

The Allen Institute for Brain Science has recently achieved some modeling milestones, which we are happy to share with the community.

1. Our paper about a biologically-realistic, data-driven model of the Layer 4 of mouse V1 has been published: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006535.

As reported in the paper, simulations of the 45,000-neuron model reproduced a variety of experimental observations, including effects of optogenetic perturbations.  Insights into the mechanisms underlying patterns of activity and computations in the Layer 4 circuit were obtained.  And, the model was developed and simulated employing both the biophysically detailed and point-neuron levels of resolution.  The model and results of simulations are freely available to the community.

2. We publicly released our software suite for model building and simulations, the Brain Modeling ToolKit (BMTK): https://alleninstitute.github.io/bmtk/.

This Python-based tool provides a powerful environment for building neuronal circuit models and a standardized interface for simulations, which interacts with other excellent tools, such as NEURON, NEST, and others.  The interface allows one to harness the power of these existing tools for large-scale network simulations, while keeping the need for software coding to the minimum.

3. The Allen Institute website now features a section on Computational Modeling and Theory: http://portal.brain-map.org/explore/models.

This site contains information and data from our published modeling papers (including the one above, but also others) and modeling software.  Please visit the site and use our resources for your work!

We hope that these tools and data will be useful for you and are looking forward to questions and feedback.

Anton Arkhipov
Associate Investigator
antona at alleninstitute.org<mailto:antona at alleninstitute.org>
T: 206.548.8414

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