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Join us at the 2023 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. Applications are now closed.
Graduate, Scientists, Undergraduate
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.
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 extracellular electric field
Using and sharing models in the SONATA format
Visualizing network models’ structure and dynamics in 3D
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 February 15. All applicants will be notified of the status of their application by April 15.
Subject to change.
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
Presentations by Allen Institute scientists and collaborators – 9:00-10:15am
Demo of BMTK, SONATA, and VND – 10:15-10:45am
Lunch, small group discussions – 12:00-2:00pm
Depart Allen Institute – 5:00pm
05.11.2023 - 05.15.2023 | 9:00AM
04.03.2023 - 04.04.2023 | 8:30AM-5:00PM
03.22.2023 | 4:00PM-6:00PM