From ddecbd8b5003b4e327e2baf57dd4796ee59b7dbc Mon Sep 17 00:00:00 2001 From: anilbey Date: Tue, 10 Oct 2023 09:43:17 +0200 Subject: [PATCH 1/4] Update README.rst Updated the publication link to be patterns --- README.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.rst b/README.rst index 42e32c9..9f4b3f3 100644 --- a/README.rst +++ b/README.rst @@ -6,7 +6,7 @@ A universal workflow for creation, validation, and generalization of detailed ne +----------------+------------+ | Build Status | |build| | +----------------+------------+ -| Zenodo | |zenodo| | +| Publication | |doi| | +----------------+------------+ Introduction @@ -161,5 +161,5 @@ For MOD files for which the original source is available on ModelDB, any specifi :target: https://github.com/BlueBrain/SSCxEModelExamples/blob/main/LICENSE.txt :alt: license -.. |zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.8220219.svg - :target: https://doi.org/10.5281/zenodo.8220219 +.. |doi| image:: https://img.shields.io/badge/DOI-10.1016/j.patter.2023.100855-blue + :target: https://doi.org/10.1016/j.patter.2023.100855 From 387455e448f7d48792cb45fc5e3e511780fbd02d Mon Sep 17 00:00:00 2001 From: Anil Tuncel Date: Tue, 10 Oct 2023 10:15:43 +0200 Subject: [PATCH 2/4] add a link to the publication in introduction --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 9f4b3f3..d148d6f 100644 --- a/README.rst +++ b/README.rst @@ -12,7 +12,7 @@ A universal workflow for creation, validation, and generalization of detailed ne Introduction --------- -The biophysically detailed electrical neuron model (e-model) is one of the central tools in neuroscience. Here we present a demo of the single neuron e-model creation, validation, and generalization described in **"A universal workflow for creation, validation, and generalization of detailed neuronal models" (Reva, Rossert et al)**. +The biophysically detailed electrical neuron model (e-model) is one of the central tools in neuroscience. Here we present a demo of the single neuron e-model creation, validation, and generalization described in `A universal workflow for creation, validation, and generalization of detailed neuronal models (Reva, Rossert et al) `_. This demo is built on the example of L5PC of the SSCx in juvenile rat. From e33c4dbe96ce65d3105954309594ed0dbfdda6da Mon Sep 17 00:00:00 2001 From: Anil Tuncel Date: Tue, 10 Oct 2023 10:37:40 +0200 Subject: [PATCH 3/4] update bibtex entry --- README.rst | 20 +++++++++----------- 1 file changed, 9 insertions(+), 11 deletions(-) diff --git a/README.rst b/README.rst index d148d6f..b532232 100644 --- a/README.rst +++ b/README.rst @@ -36,17 +36,15 @@ A universal workflow for creation, validation, and generalization of detailed ne .. code-block:: - @ARTICLE{Reva2022.12.13.520234, - author = {Reva, Maria and R{\"o}ssert, Christian and Arnaudon, Alexis and Damart, Tanguy and Mandge, Darshan and Tuncel, An{\i}l and Ramaswamy, Srikanth and Markram, Henry and Van Geit, Werner}, - title = {A universal workflow for creation, validation and generalization of detailed neuronal models}, - elocation-id = {2022.12.13.520234}, - year = {2022}, - doi = {10.1101/2022.12.13.520234}, - publisher = {Cold Spring Harbor Laboratory}, - abstract = {Detailed single neuron modeling is widely used to study neuronal functions. While cellular and functional diversity across the mammalian cortex is vast, most of the available computational tools are dedicated to the reproduction of a small set of specific features characteristic of a single neuron. Here, we present a generalized automated workflow for the creation of robust electrical models and illustrate its performance by building cell models for the rat somatosensory cortex (SSCx). Each model is based on a 3D morphological reconstruction and a set of ionic mechanisms specific to the cell type. We use an evolutionary algorithm to optimize passive and active ionic parameters to match the electrophysiological features extracted from whole-cell patch-clamp recordings. To shed light on which parameters are constrained by experimental data and which could be degenerate, we perform a parameter sensitivity analysis. We also validate the optimized models against additional experimental stimuli and assess their generalizability on a population of morphologies with the same morphological type. With this workflow, we generate SSCx neuronal models producing the variability of neuronal responses. Due to its versatility, our workflow can be used to build robust biophysical models of any neuronal type.Competing Interest StatementThe authors have declared no competing interest.}, - URL = {https://www.biorxiv.org/content/early/2022/12/13/2022.12.13.520234}, - eprint = {https://www.biorxiv.org/content/early/2022/12/13/2022.12.13.520234.full.pdf}, - journal = {bioRxiv} + @article{reva2023universal, + title={A universal workflow for creation, validation, and generalization of detailed neuronal models}, + author={Reva, Maria and R{\"o}ssert, Christian and Arnaudon, Alexis and Damart, Tanguy and Mandge, Darshan and Tuncel, An{\i}l and Ramaswamy, Srikanth and Markram, Henry and Van Geit, Werner}, + journal={Patterns}, + publisher={Elsevier}, + doi={10.1016/j.patter.2023.100855}, + url={https://doi.org/10.1016/j.patter.2023.100855}, + issn={2666-3899}, + year={2023} } Pipeline From 3a8575ef18876492899340879d74ff5c80c5fe24 Mon Sep 17 00:00:00 2001 From: Anil Tuncel Date: Tue, 10 Oct 2023 10:52:26 +0200 Subject: [PATCH 4/4] update bluepymm>=0.9.7 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index efbf7d5..35bec45 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,5 +6,5 @@ numpy<1.24 NEURON>=7.8.0,<8.0.0 matplotlib seaborn -bluepymm>=0.8 +bluepymm>=0.9.7 jupyter