Events

2022 Allen Institute Modeling Software Workshop

Join us at the Allen Institute Modeling Software Workshop for a hands-on opportunity to learn how to use open-source software modeling tools developed in part at the Allen Institute MindScope Program. In this workshop, attendees will learn how to use software for building, simulating, and visualizing bio-realistic models of brain circuits. These tools include:

  • 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.

None

07/25/2022 to 07/26/2022

This two-day 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.

We are eager to host a diverse audience, and we encourage trainees, scientists, and PIs to apply.

Preference 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.

Applications are due on March 15. All applicants will be notified of the status of their application by May 20.

Applications are now closed for the 2022 workshop. We anticipate holding the workshop again in 2023.

*If conducting the workshop in person becomes impossible due to covid-related safety concerns, it will be replaced by an online workshop on the same dates.

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

Tentative Workshop Schedule

Schedule is subject to change.

Monday, July 25, 2022

Session

Time

Welcome, registration, and breakfast

8:30am

Workshop introduction and overview

9:00-9:45am

Software environment setup

9:45-10:00am

Demo of BMTK, SONATA, and VND

10:00-10:45am

Break

10:45-11:00am

Continued - demo of BMTK, SONATA, and VND

11:00am-12:00pm

Lunch, participant introductions, and meet & greet

12:00-2:00pm

Participants work on tutorials

2:00-3:30pm

Break

3:30-3:45pm

Continued - participants work on tutorials

3:45-5:00pm

Tour of the Allen Institute

5:00-5:30pm

Dinner

5:30pm

 

Tuesday, July 26, 2022

Session

Time

Presentations by Allen Institute scientists and collaborators

9:00-10:15am

Demo of BMTK, SONATA, and VND 10:15-10:45am

Break

10:45-11:00am

Continued - demo of BMTK, SONATA, and VND

11:00am-12:00pm

Lunch, small group discussions

12:00-2:00pm

Participants work on tutorials

2:00-3:30pm

Break

3:30-3:45pm

Continued - participants work on tutorials

3:45-5:00pm

Depart Allen Institute

5:00pm

0