#computationalmodelling — Public Fediverse posts

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

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

If you're seeing your #NEST simulator builds fail recently, it's because of a new #Cython release:

https://github.com/nest/nest-simulator/issues/3495

Workaround: fix `cython<3.1.0` for the moment (until new NEST releases with the fix are made)

#ComputationalNeuroscience #ComputationalModelling #Neuroscience #AcademicChatter

Generated a quick plot to see usage trends for Open Source Brain v2 (#OSBv2): an integrated #research platform for #neuroscience that indexes multiple model and data sources (#DANDI, #ModelDB, #Biomodels, #Github) and provides compute resources on the #cloud in "workspaces". It also includes specialist applications: #NWBExplorer for working with data in the NeuroData Without Borders (#NWB) format; #NetPyNE-UI for biophysically detailed #ComputationalModelling and a #JupyterLab environment.

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

Estimate of excess deaths attributable to global warming during hot summer of 2022 in Europe: between about 22000 and 59000.
A small city wiped out.
https://www.nature.com/articles/s41612-024-00783-2

#globalwarming #computationalmodelling

Estimate of excess deaths attributable to global warming during hot summer of 2022 in Europe: between about 22000 and 59000.
A small city wiped out.
https://www.nature.com/articles/s41612-024-00783-2

#globalwarming #computationalmodelling

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

My *psp* package received some new updates and bug fixes 🥳🥳 check it out here:

https://cran.r-project.org/web/packages/psp/index.html

#R #rstats #computationalmodelling #cognitivescience

The #Izhikevichmodel is a powerful tool for simulating the #spiking and bursting behavior of #neurons with a remarkable balance between biological relevance and computational efficiency 💫 Here is a short introduction along with a #Python implementation to simulate various types of #cortical neurons, including regular spiking, fast spiking, and bursting neurons:

🌍 https://www.fabriziomusacchio.com/blog/2024-04-29-izhikevich_model/

Feel free to share and experiment with it ☺️

#CompNeuro #ComputationalModelling #ComputationalNeuroscience

The #Izhikevichmodel is a powerful tool for simulating the #spiking and bursting behavior of #neurons with a remarkable balance between biological relevance and computational efficiency 💫 Here is a short introduction along with a #Python implementation to simulate various types of #cortical neurons, including regular spiking, fast spiking, and bursting neurons:

🌍 https://www.fabriziomusacchio.com/blog/2024-04-29-izhikevich_model/

Feel free to share and experiment with it ☺️

#CompNeuro #ComputationalModelling #ComputationalNeuroscience

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

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

4/
A general issue concerns seductive #research black-box tools (or, equivalently, trending methods "inspired" by published works one doesn't really understand): easy to incur #overfitting, which implies modelling not only the "signal" being studied in too few data, but also (or mostly) their useless noise.

Recursive: if we fall into the trap (no proper #validation), our readers may be led to believe that these shortcuts have a chance to work, perpetuating anti-culture.

#ComputationalModelling

4/
A general issue concerns seductive #research black-box tools (or, equivalently, trending methods "inspired" by published works one doesn't really understand): easy to incur #overfitting, which implies modelling not only the "signal" being studied in too few data, but also (or mostly) their useless noise.

Recursive: if we fall into the trap (no proper #validation), our readers may be led to believe that these shortcuts have a chance to work, perpetuating anti-culture.

#ComputationalModelling

1/
A concerning post-publication exercise (which led the original flawed publication to #retraction) on how easy is for our "intuition" of #ComputationalModelling to deceive ourselves and others

Here, "others" seem to include editors and some reviewers (whose expertise maybe was not directly in modelling) of a respected journal. Plus readers who cited a flawed work and propagated the flaw

Comments:
@kordinglab - coauth. @tdverstynen
https://neuromatch.social/@kordinglab/110155049278014769

@erinnacland
https://fediscience.org/@erinnacland/110514563951876284

1/
A concerning post-publication exercise (which led the original flawed publication to #retraction) on how easy is for our "intuition" of #ComputationalModelling to deceive ourselves and others

Here, "others" seem to include editors and some reviewers (whose expertise maybe was not directly in modelling) of a respected journal. Plus readers who cited a flawed work and propagated the flaw

Comments:
@kordinglab - coauth. @tdverstynen
https://neuromatch.social/@kordinglab/110155049278014769

@erinnacland
https://fediscience.org/@erinnacland/110514563951876284

On the 🇪🇺 Day of Languages find out how @kennysmithed and the research team @EdinburghUni use a combination of experiments & #computationalmodelling to uncover some big ideas in #evolutionary #linguistics.

Read 👉 http://bit.ly/3Re3DRh

@CORDIS_EU @cogsci_soc #languagelearning

🐦🔗: https://nitter.eu/ERC_Research/status/1574300191389548544