Mastodawn

A new version of the Open Source Brain (#OpenSourceBrain) model validation framework was just released. Please update your installations:

```
pip install -U OSBModelValidation
```

https://github.com/OpenSourceBrain/osb-model-validation/releases/tag/v0.3.9

#OMV is a #Python package that allows you to validate your #NeuroML models against different simulation engines---to ensure that you get the same behaviours on all these engines. Examples:

https://github.com/OpenSourceBrain/.github/blob/main/testsheet/README.md

#FAIR #ComputationalNeuroscience #Neuroscience #ModelValidation

Release v0.3.9 · OpenSourceBrain/osb-model-validation

What's Changed Main tests run on py 3.11; use updated moose & neuron by @pgleeson in #139 Feat: remove double error printing by @sanjayankur31 in #144 Feat: use jnml from pyneuroml by @sanjayankur...

GitHub

Ankur Sinha "FranciscoD"Mar 5

#NeuroML is participating in #GSoC2025 again this year under @INCF . We're looking for people with some experience of #ComputationalNeuroscience to work on developing #standardised biophysically detailed computational models using #NeuroML #PyNN and #OpenSourceBrain.

Please spread the word, especially to students interested in modelling. We will help them learn the NeuroML ecosystem so they can use its standardised pipeline in their work.

https://docs.neuroml.org/NeuroMLOrg/OutreachTraining.html#google-summer-of-code

CC #AcademicChatter

Outreach and training — NeuroML Documentation

Ankur Sinha "FranciscoD"Sep 11, 2024

Update on what I did from weeks 27-36 this year:

https://ankursinha.in/2024/09/06/week-27-36-update.html

#NeuroML #ComputationalNeuroscience #Fedora #OpenSourceBrain #GoogleSummerOfCode #ComputationalModelling #AcademicChatter #FOSS #OpenScience

Week 27--36 update - ankursinha.in/blog

Ankur Sinha "FranciscoD"Sep 11, 2024

#Standardized #NeuroML model of the day (2024-09-11):

Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties, Hay et al 2011

See if on #OpenSourceBrain here:

https://v1.opensourcebrain.org/projects/l5bpyrcellhayetal2011

and on #GitHub here: https://github.com/OpenSourceBrain/L5bPyrCellHayEtAl2011

#ComputationalNeuroscience #ComputationalModelling #Neuroscience #Cortex #Layer5B #FAIR #OpenScience #AcademicChatter

Learn more about NeuroML here: https://docs.neuroml.org

Overview - Layer 5b Pyramidal cell - Hay et al. 2011 - Open Source Brain

Open Source Brain is a resource for sharing and collaboratively developing computational models of neural systems.

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Ankur Sinha "FranciscoD"Feb 24, 2023

We're *also* looking for candidates to work with us at #GSoC2023 on the conversion of published neuroscience data into the #NeurodataWithoutBorders standard format. Please spread the word, and get in touch!

https://neurostars.org/t/gsoc-2023-project-idea-21-2-open-source-brain-conversion-of-public-neurophysiology-datasets/24922

#INCF #FAIR #Neuroscience #Standardisation #OpenSourceBrain

GSoC 2023 Project Idea 21.2 Open Source Brain - Conversion of public neurophysiology datasets

Title: Conversion of public neurophysiology datasets to Neurodata Without Borders (NWB) format Description: More and more of the experimental datasets behind publications in neuroscience are being publicly released, increasing transparency of the scientific process and allowing reuse of the data for new investigations. However, these datasets, which can include electrophysiology, 2D/3D imaging data and behavioural recordings, are not always in an accessible format, and it may take some effort ...

Neurostars

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Ankur Sinha "FranciscoD"Feb 1, 2023

@gabrock94 I think either would do as long as it's well commented. The advantage with Jupyter notebooks is that one can use Binder/Google Collab etc. to run them without requiring a local setup.

We're also developing a new version of #OpenSourceBrain where one can keep their data + code and use a full #JupyterLab environment on our cloud instance:

https://v2.opensourcebrain.org

(Under heavy development, still Beta!)

Open Source Brain

Ankur Sinha "FranciscoD"Jan 23, 2023

FYI folks, the Open Source Brain cluster is being upgraded and migrated, so you may experience transient issues on the #OpenSourceBrain platforms. More information on the status page here:

https://status.opensourcebrain.org/

#OpenScience #Neuroscience #Neuroinformatics #NetPyNE #NWBExplorer

CC: @sdurabernal