#neuroml — Public Fediverse posts

Building detailed neuronal models is hard---#NeuroML helps, but there’s still a steep learning curve. We're investigating how #LLMs can be used to create natural language interfaces to improve accessibility:

- #RAG for NeuroML: learn from and query curated information sources
- iterative LLM assisted code/model generation: modelling, validation, and simulation

More details in the post:

https://ankursinha.in/2026/01/30/building-an-ai-assistant-for-computational-modelling-with-neuroml.html

#Neuroscience #ComputationalNeuroscience #AcademicChatter #LangChain

I created a #CookieCutter project template for #ComputationalModelling using #NeuroML

(You can use it for non NeuroML models too, or modify it for your own templates)

More information here:

https://ankursinha.in/2025/09/23/a-cookiecutter-template-to-quickstart-neuroml-modelling-projects.html

#ComputationalNeuroscience #Python #Neuroscience #AcademicChatter

I created a #CookieCutter project template for #ComputationalModelling using #NeuroML

(You can use it for non NeuroML models too, or modify it for your own templates)

More information here:

https://ankursinha.in/2025/09/23/a-cookiecutter-template-to-quickstart-neuroml-modelling-projects.html

#ComputationalNeuroscience #Python #Neuroscience #AcademicChatter

I created a #CookieCutter project template for #ComputationalModelling using #NeuroML

(You can use it for non NeuroML models too, or modify it for your own templates)

More information here:

https://ankursinha.in/2025/09/23/a-cookiecutter-template-to-quickstart-neuroml-modelling-projects.html

#ComputationalNeuroscience #Python #Neuroscience #AcademicChatter

I created a #CookieCutter project template for #ComputationalModelling using #NeuroML

(You can use it for non NeuroML models too, or modify it for your own templates)

More information here:

https://ankursinha.in/2025/09/23/a-cookiecutter-template-to-quickstart-neuroml-modelling-projects.html

#ComputationalNeuroscience #Python #Neuroscience #AcademicChatter

I created a #CookieCutter project template for #ComputationalModelling using #NeuroML

(You can use it for non NeuroML models too, or modify it for your own templates)

More information here:

https://ankursinha.in/2025/09/23/a-cookiecutter-template-to-quickstart-neuroml-modelling-projects.html

#ComputationalNeuroscience #Python #Neuroscience #AcademicChatter

A lot of steps for starting new computational modelling projects in #NeuroML are repeatable and can be automated. So, I created a #Cookiecutter template to quickstart these projects. It includes boilerplate code and implements lots of other recommended/best practices in model and software development. Feedback/suggestions welcome!

https://ankursinha.in/2025/09/23/a-cookiecutter-template-to-quickstart-neuroml-modelling-projects.html

#Neuroscience #ComputationalNeuroscience #Python #Git #AcademicChatter #FAIR #OpenScience #FOSS #SoftwareDevelopment

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

A new release of #PyNeuroML is available. Please update to get the latest fixes and features. #NeuroML #ComputationalModelling #ComputationalNeuroscience

```
pip install --upgrade pyneuroml
```

A new release of #PyNeuroML is available. Please update to get the latest fixes and features. #NeuroML #ComputationalModelling #ComputationalNeuroscience

```
pip install --upgrade pyneuroml
```

A new release of #PyNeuroML is available. Please update to get the latest fixes and features. #NeuroML #ComputationalModelling #ComputationalNeuroscience

```
pip install --upgrade pyneuroml
```

A new release of #PyNeuroML is available. Please update to get the latest fixes and features. #NeuroML #ComputationalModelling #ComputationalNeuroscience

```
pip install --upgrade pyneuroml
```

A new release of #PyNeuroML is available. Please update to get the latest fixes and features. #NeuroML #ComputationalModelling #ComputationalNeuroscience

```
pip install --upgrade pyneuroml
```

#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

#NeuroML supports all stages of the modelling life-cycle with a vast ecosystem of software tools: creating (#pyNeuroML, #neuroConstruct, #NEURON, #NetPyNE, #PyNN, #N2A), validating (pyNeuroML, #OMV, #SciUnit), visualising (pyNeuroML, #OSB, #NeuroML-DB), simulating (#NEURON, #NetPyNE, #Brian, #PyNN, #NEST, #MOOSE, #EDEN), model fitting/optimisation (#NeuroTune, #BluePyOpt, NetPyNE), sharing and reusing of models (OSB, NeuroML-DB, #NeuroMorpho.org). 7/x

#NeuroML supports all stages of the modelling life-cycle with a vast ecosystem of software tools: creating (#pyNeuroML, #neuroConstruct, #NEURON, #NetPyNE, #PyNN, #N2A), validating (pyNeuroML, #OMV, #SciUnit), visualising (pyNeuroML, #OSB, #NeuroML-DB), simulating (#NEURON, #NetPyNE, #Brian, #PyNN, #NEST, #MOOSE, #EDEN), model fitting/optimisation (#NeuroTune, #BluePyOpt, NetPyNE), sharing and reusing of models (OSB, NeuroML-DB, #NeuroMorpho.org). 7/x

#NeuroML supports all stages of the modelling life-cycle with a vast ecosystem of software tools: creating (#pyNeuroML, #neuroConstruct, #NEURON, #NetPyNE, #PyNN, #N2A), validating (pyNeuroML, #OMV, #SciUnit), visualising (pyNeuroML, #OSB, #NeuroML-DB), simulating (#NEURON, #NetPyNE, #Brian, #PyNN, #NEST, #MOOSE, #EDEN), model fitting/optimisation (#NeuroTune, #BluePyOpt, NetPyNE), sharing and reusing of models (OSB, NeuroML-DB, #NeuroMorpho.org). 7/x

#NeuroML supports all stages of the modelling life-cycle with a vast ecosystem of software tools: creating (#pyNeuroML, #neuroConstruct, #NEURON, #NetPyNE, #PyNN, #N2A), validating (pyNeuroML, #OMV, #SciUnit), visualising (pyNeuroML, #OSB, #NeuroML-DB), simulating (#NEURON, #NetPyNE, #Brian, #PyNN, #NEST, #MOOSE, #EDEN), model fitting/optimisation (#NeuroTune, #BluePyOpt, NetPyNE), sharing and reusing of models (OSB, NeuroML-DB, #NeuroMorpho.org). 7/x

We are very happy to provide a consolidated update on the #NeuroML ecosystem in our @eLife paper, “The NeuroML ecosystem for standardized multi-scale modeling in neuroscience”: https://doi.org/10.7554/eLife.95135.3

#NeuroML is a standard and software ecosystem for data-driven biophysically detailed #ComputationalModelling endorsed by the @INCF and CoMBINE, and includes a large community of users and software developers.

#Neuroscience #ComputationalNeuroscience #ComputationalModelling 1/x

We are very happy to provide a consolidated update on the #NeuroML ecosystem in our @eLife paper, “The NeuroML ecosystem for standardized multi-scale modeling in neuroscience”: https://doi.org/10.7554/eLife.95135.3

#NeuroML is a standard and software ecosystem for data-driven biophysically detailed #ComputationalModelling endorsed by the @INCF and CoMBINE, and includes a large community of users and software developers.

#Neuroscience #ComputationalNeuroscience #ComputationalModelling 1/x

We are very happy to provide a consolidated update on the #NeuroML ecosystem in our @eLife paper, “The NeuroML ecosystem for standardized multi-scale modeling in neuroscience”: https://doi.org/10.7554/eLife.95135.3

#NeuroML is a standard and software ecosystem for data-driven biophysically detailed #ComputationalModelling endorsed by the @INCF and CoMBINE, and includes a large community of users and software developers.

#Neuroscience #ComputationalNeuroscience #ComputationalModelling 1/x

We are very happy to provide a consolidated update on the #NeuroML ecosystem in our @eLife paper, “The NeuroML ecosystem for standardized multi-scale modeling in neuroscience”: https://doi.org/10.7554/eLife.95135.3

#NeuroML is a standard and software ecosystem for data-driven biophysically detailed #ComputationalModelling endorsed by the @INCF and CoMBINE, and includes a large community of users and software developers.

#Neuroscience #ComputationalNeuroscience #ComputationalModelling 1/x

We are very happy to provide a consolidated update on the #NeuroML ecosystem in our @eLife paper, “The NeuroML ecosystem for standardized multi-scale modeling in neuroscience”: https://doi.org/10.7554/eLife.95135.3

#NeuroML is a standard and software ecosystem for data-driven biophysically detailed #ComputationalModelling endorsed by the @INCF and CoMBINE, and includes a large community of users and software developers.

#Neuroscience #ComputationalNeuroscience #ComputationalModelling 1/x

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

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

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

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

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

#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

#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

#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

#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

#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

The latest release of #PyNeuroML, 1.3.9, includes `pynml-swc2nml` for conversion of #SWC neuronal morphologies to #NeuroML. Also accessible via the API:

https://pyneuroml.readthedocs.io/en/development/pyneuroml.swc.html#pyneuroml.swc.ExportNML.convert_swc_to_neuroml

Install it using pip:

https://pypi.org/project/pyNeuroML/1.3.9/

#NeuroML #ComputationalNeuroscience #NeuronalModelling #FAIR #Neuroscience #AcademicChatter

The latest release of #PyNeuroML, 1.3.9, includes `pynml-swc2nml` for conversion of #SWC neuronal morphologies to #NeuroML. Also accessible via the API:

https://pyneuroml.readthedocs.io/en/development/pyneuroml.swc.html#pyneuroml.swc.ExportNML.convert_swc_to_neuroml

Install it using pip:

https://pypi.org/project/pyNeuroML/1.3.9/

#NeuroML #ComputationalNeuroscience #NeuronalModelling #FAIR #Neuroscience #AcademicChatter

The latest release of #PyNeuroML, 1.3.9, includes `pynml-swc2nml` for conversion of #SWC neuronal morphologies to #NeuroML. Also accessible via the API:

https://pyneuroml.readthedocs.io/en/development/pyneuroml.swc.html#pyneuroml.swc.ExportNML.convert_swc_to_neuroml

Install it using pip:

https://pypi.org/project/pyNeuroML/1.3.9/

#NeuroML #ComputationalNeuroscience #NeuronalModelling #FAIR #Neuroscience #AcademicChatter

How's Friday going folks? I've been working on standardising the #Purkinje Cell model from Zang et al 2018 to #NeuroML. Exported the morphology already, on to the converting the individual Ion channels next.

You can use the converted bits from here: https://github.com/sanjayankur31/ZangEtAl2018/tree/development

#Neuroscience #ComputationalNeuroscience #Modelling #ComputationalModelling #Cerebellum

How's Friday going folks? I've been working on standardising the #Purkinje Cell model from Zang et al 2018 to #NeuroML. Exported the morphology already, on to the converting the individual Ion channels next.

You can use the converted bits from here: https://github.com/sanjayankur31/ZangEtAl2018/tree/development

#Neuroscience #ComputationalNeuroscience #Modelling #ComputationalModelling #Cerebellum

How's Friday going folks? I've been working on standardising the #Purkinje Cell model from Zang et al 2018 to #NeuroML. Exported the morphology already, on to the converting the individual Ion channels next.

You can use the converted bits from here: https://github.com/sanjayankur31/ZangEtAl2018/tree/development

#Neuroscience #ComputationalNeuroscience #Modelling #ComputationalModelling #Cerebellum

How's Friday going folks? I've been working on standardising the #Purkinje Cell model from Zang et al 2018 to #NeuroML. Exported the morphology already, on to the converting the individual Ion channels next.

You can use the converted bits from here: https://github.com/sanjayankur31/ZangEtAl2018/tree/development

#Neuroscience #ComputationalNeuroscience #Modelling #ComputationalModelling #Cerebellum

How's Friday going folks? I've been working on standardising the #Purkinje Cell model from Zang et al 2018 to #NeuroML. Exported the morphology already, on to the converting the individual Ion channels next.

You can use the converted bits from here: https://github.com/sanjayankur31/ZangEtAl2018/tree/development

#Neuroscience #ComputationalNeuroscience #Modelling #ComputationalModelling #Cerebellum

Version 1.2.0 of #pyNeuroML, the #Python package for working with #NeuroML models, has been released, brings more bugfixes and better support for #SBML

https://github.com/NeuroML/pyNeuroML/releases/tag/v1.2.0

#NeuroML #ComputationalNeuroscience #Neuroscience #Standardisation #FAIR

https://www.biorxiv.org/content/10.1101/2023.12.07.570537v1

The #NeuroML ecosystem for standardized multi-scale modeling in neuroscience

#ComputationalNeuroscience #Neuroscience #Modelling #ComputationalModelling #AcademicChatter

https://www.biorxiv.org/content/10.1101/2023.12.07.570537v1

The #NeuroML ecosystem for standardized multi-scale modeling in neuroscience

#ComputationalNeuroscience #Neuroscience #Modelling #ComputationalModelling #AcademicChatter

https://www.biorxiv.org/content/10.1101/2023.12.07.570537v1

The #NeuroML ecosystem for standardized multi-scale modeling in neuroscience

#ComputationalNeuroscience #Neuroscience #Modelling #ComputationalModelling #AcademicChatter

https://www.biorxiv.org/content/10.1101/2023.12.07.570537v1

The #NeuroML ecosystem for standardized multi-scale modeling in neuroscience

#ComputationalNeuroscience #Neuroscience #Modelling #ComputationalModelling #AcademicChatter

https://www.biorxiv.org/content/10.1101/2023.12.07.570537v1

The #NeuroML ecosystem for standardized multi-scale modeling in neuroscience

#ComputationalNeuroscience #Neuroscience #Modelling #ComputationalModelling #AcademicChatter

Please boost:

Please join us for the next open #NeuroML editorial team meeting on March 30 at 1600 UTC:

More information (and meeting link) in the agenda document here:

https://hackmd.io/drmamFWvSMibBA-SiVPWGg

#Neuroscience #OpenScience #ComputationalNeuroscience #INCF

We're looking for candidates to work with us at #GSoC2023 on conversion of published #ComputationalNeuroscience models into #NeuroML and #PyNN standard formats. Please spread the word, and get in touch!

https://neurostars.org/t/gsoc-2023-project-idea-21-1-open-brain-cross-simulator-large-scale-cortical-models-in-neuroml-and-pynn/24921

#INCF #Standardisation #FAIR #Neuroscience #Replication

Membrane potentials in a L23 human #PyramidalNeuron model using #NeuroML tools. So cool!

https://imgur.com/a/z26Z3wp

#Neuroscience #ComputationalNeuroscience