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2024 Allen Institute Modeling Software Workshop


Join us at the 2024 Allen Institute Modeling Software Workshop for a hands-on opportunity to learn how to use open-source software modeling tools developed by the Allen Institute and our collaborators at the University of Illinois Urbana-Champaign (UIUC).

The deadline for applying for this workshop has passed. All applicants will be notified of the status of their application by May 1.

Jul 15 - 17, 2024

Allen Institute


Graduate, Scientists, Undergraduate

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About This Event

Workshop Topics

  • Building heterogenous neural networks at different levels of resolution

  • Simulating networks of biophysically detailed, compartmental neuronal models

  • Simulating networks of point-neuron models

  • Providing realistic spiking inputs to the neural networks

  • Simulating perturbations

  • Simulating extracellular electric field

  • Using and sharing models in the SONATA format

  • Visualizing network models’ structure and dynamics in 3D

Attendees will learn how to use software for building, simulating, and visualizing bio-realistic models of brain circuits including:

  • The SONATA file format for multiscale neuronal network models and simulation output, supporting standardized and computationally efficient storage and exchange of models.

  • The Brain Modeling ToolKit (BMTK) – a Python-based software package for building and simulating large-scale neural network models at multiple levels of resolution.

  • The Visual Neuronal Dynamics (VND) – a program for displaying, animating, and analyzing neural network models using 3D graphics and built-in scripting.




This in-person workshop will consist of interactive seminars and hands-on computational work. It will focus on teaching the skills for building and simulating complex and heterogeneous network models grounded in real biological data.

The deadline for applying for this workshop has passed. All applicants will be notified of the status of their application by May 1.

230,000-neuron model of mouse V1 with modeled neurons of different colors flashing based on their stimuli during the gifPreference will be given to those applicants who are actively doing research in computational neuroscience or are preparing to start a research project in this area. Note that some prior experience with Python might be useful for this workshop. Experience in modeling is not required or expected.

The Allen Institute strives to make training opportunities available on a fair and equitable basis. Some travel funding is available for participants with financial need. Please indicate on your application whether such support is needed. Applications will be evaluated on a need-blind basis. There is no fee to participate in the workshop.

This work was supported by the National Institute Of Biomedical Imaging And Bioengineering of the National Institutes of Health under Award Number R01EB029813 and the National Institute Of Neurological Disorders And Stroke of the National Institutes of Health under Award Numbers R01NS122742 and U24NS124001. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Science Programs at Allen Institute