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:
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The SONATA file format for multiscale neuronal network models and simulation output, supporting standardized and computationally efficient storage and exchange of models.
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The Brain Modeling ToolKit (BMTK) – a Python-based software package for building and simulating large-scale neural network models at multiple levels of resolution.
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The Visual Neuronal Dynamics (VND) – a program for displaying, animating, and analyzing neural network models using 3D graphics and built-in scripting.
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.
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Simulating perturbations
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Simulating extracellular electric field
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Using and sharing models in the SONATA format
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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 |
|
Break |
9:45-10:00am |
|
Software environment setup |
10:00-10:15am |
|
Demo of BMTK, SONATA, and VND |
10:15-11:00am |
|
Break |
11:00-11:15am |
| Continued - demo of BMTK, SONATA, and VND |
11:15am-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 |
|
Invited speaker (TBA) |
9:00-9:45am |
|
Break |
9:45-10:00am |
|
Presentations by Allen Institute scientists and collaborators |
10:00-10:45am |
|
Break |
10:45-11:00am |
| Demo of advanced features of VND for rendering and videos |
11:15am-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 |