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:
#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
Job - Alert 🚀
🎓 PHD STUDENT (F/M/D) IN MICROSTRUCTURE MODELLING AND UPSCALING
Deadline: 2024-11-28
Location: Germany, Freiberg, Sachsen
APPLY: https://www.academiceurope.com/job/?id=5854
#hiring #computationalmodelling #geophysicalsciences #Geosciences #MathematicalModelling #PhD #Statistics
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
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:
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.
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
Check out these post-doc opportunities in the mechanisms of social behavior group (at Karolinska Institute, Stockholm), led by https://twitter.com/B_Lindstroem
https://ki.varbi.com/en/what:job/jobID:576453/
#jobs #cognition #sociallearning #computationalmodelling #culturalevolution
Hola all, I'll primarily be posting about #cognitive #neuroscience #mentalhealth #computationalmodelling #psychiatry #anxiety #depression #neuroimaging #fMRI but occasionally about parochial East London concerns 👋
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
