Allen Institute Modeling Software Workshop

This two-day, in-person workshop, taking place on July 13-14, 2023, provides a hands-on opportunity to learn how to use software tools developed in part at the Allen institute. Applications are due February 15, 2023. 

The Allen Institute, a BRAIN Initiative Alliance (BIA) partner, is hosting the Allen Institute Modeling Software Workshop on July 13-14, 2023. This two-day, in-person workshop at the Allen Institute will consist of interactive seminars and hands-on computational work using open-source software modeling tools. Attendees will learn how to use these software tools for building, simulating, and visualizing bio-realistic models of brain circuits. The software tools include: 

  • SONATA – a file format for neuronal network models and simulation output, supporting standardized and computationally efficient storage and exchange of models 

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

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

The featured software tools, Brain Modeling Tools: BMTK, SONATA, VND, are included in the BIA’s Toolmakers Resources

Additional workshop topics include: 

  • Building heterogeneous 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  

For the full agenda and registration information, please visit the event webpage

Trainees, scientists, and principal investigators are encouraged to apply. Applications are due by February 15, 2023. All applicants will be notified of the status of their application by April 15, 2023. 

This workshop is being supported by NIH BRAIN Dissemination Program grant U24NS124001

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Allen Institute
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