diff --git a/.cspell_dict.txt b/.cspell_dict.txt index 1690e54..48dae4e 100644 --- a/.cspell_dict.txt +++ b/.cspell_dict.txt @@ -23,6 +23,7 @@ DOLFINx elastodynamics electrodiffusive Empagliflozin +endfeet ffian finsberg Finsberg @@ -30,15 +31,18 @@ Forsch Fouilloux geometriesx Gjerde +gliovascular glymphatic gotranx Graphnics Haubner +herlyng howpublished htmlcov idealised importlib Ingeborg +insilico Jørgen jorgensd Jupyterbook @@ -66,7 +70,9 @@ odeigah oneline orcid peaceiris +periarterial perivascular +perivenous postprocess poulain Pycodestyle @@ -75,15 +81,19 @@ pypi pyproject pytest Ragan +Ratbrain +riseth saetra Sætra scientificcomputing scifem +silico Simcardems Simula Stankelbein SVMTK Valnes venv +vinje zapf Zenodo diff --git a/docs/datasets.md b/docs/datasets.md new file mode 100644 index 0000000..87c0516 --- /dev/null +++ b/docs/datasets.md @@ -0,0 +1,28 @@ +# Datasets + +This page contains a list of relevant datasets for Scientific Computing. + +## Brain MRI and Meshes + +- **[Gonzo Dataset](https://zenodo.org/records/14266867)** + Human Brain MRI Data of CSF Tracer Evolution Over 72h For Data-Integrated Simulations. + +- **[Ratbrain mesh](https://zenodo.org/records/8138343)** + Mesh files for rat brain simulations. + +- **[MRI2FEM data set](https://zenodo.org/records/4899120)** + Data set supporting the MRI2FEM book and workflows. + +## Solute Transport and Mechanics + +- **[Human brain solute transport meshes](https://zenodo.org/records/8036492)** + Example meshes for 'Human brain solute transport quantified by glymphatic MRI-informed biophysics during sleep and sleep deprivation'. + +- **[Perivascular space meshes](https://zenodo.org/records/4629927)** + Mesh files for idealized and image-based periarterial and perivenous spaces. + +- **[Mechanisms behind PVS flow](https://zenodo.org/records/3890133)** + Data related to mechanisms behind flow in perivascular spaces. + +- **[Geometrically reduced PVS flow](https://zenodo.org/records/5729458)** + Data for geometrically reduced modelling of pulsatile flow. diff --git a/docs/myst.yml b/docs/myst.yml index 247ee0f..9867135 100644 --- a/docs/myst.yml +++ b/docs/myst.yml @@ -10,9 +10,7 @@ project: - Numerical Analysis - High Performance Computing - Simulation - authors: - - Henrik Finsberg - - Jørgen Dokken + github: https://github.com/scientificcomputing/scientificcomputing.github.io # To autogenerate a Table of Contents, run "jupyter book init --write-toc" toc: @@ -21,6 +19,7 @@ project: children: - file: repositories.md - file: packages.md + - file: datasets.md - title: Guidelines for papers with code children: - file: papers-with-code.md diff --git a/docs/references.bib b/docs/references.bib index 0f5fb56..448d83e 100644 --- a/docs/references.bib +++ b/docs/references.bib @@ -52,6 +52,23 @@ @article{causemann2022 publisher = {Cold Spring Harbor Laboratory}, journal = {bioRxiv} } +@article{causemann2025insilico, + title = {In-silico molecular enrichment and clearance of the human intracranial space}, + author = {Causemann, Marius and Kuchta, Miroslav and Masri, Rami and Rognes, Marie E.}, + journal = {bioRxiv}, + year = {2025}, + doi = {10.1101/2025.01.30.635680}, + url = {https://doi.org/10.1101/2025.01.30.635680} +} +@article{causemann2025stretch, + title = {Stretch and flow at the gliovascular interface: high-fidelity modelling of the mechanics of astrocyte endfeet}, + author = {Causemann, Marius and Enger, Rune and Rognes, Marie E}, + journal = {bioRxiv}, + pages = {2025--05}, + year = {2025}, + publisher = {Cold Spring Harbor Laboratory}, + doi = {10.1101/2025.05.08.652799} +} @article{daversin2022, author = {Daversin-Catty, C\'{e}cile and Gjerde, Ingeborg G. and Rognes, Marie E.}, title = {{Geometrically Reduced Modelling of Pulsatile Flow in Perivascular Networks}}, @@ -116,6 +133,17 @@ @article{haubner2023 year = {2023}, doi = {10.1137/21M143114X} } +@article{herlyng2025advection, + title = {Advection versus diffusion in brain ventricular transport}, + author = {Herlyng, Halvor and Ellingsrud, Ada J and Kuchta, Miroslav and Jeong, Inyoung and Rognes, Marie E and Jurisch-Yaksi, Nathalie}, + journal = {Fluids and Barriers of the CNS}, + volume = {22}, + number = {1}, + pages = {82}, + year = {2025}, + publisher = {Springer}, + doi = {10.1186/s12987-025-00692-3} +} @article{https://doi.org/10.1002/cnm.2982, author = {Finsberg, Henrik and Xi, Ce and Tan, Ju Le and Zhong, Liang and Genet, Martin and Sundnes, Joakim and Lee, Lik Chuan and Wall, Samuel T.}, title = {Efficient estimation of personalized biventricular mechanical function employing gradient-based optimization}, @@ -194,6 +222,17 @@ @article{odeigah2024computational year = {2024}, publisher = {Frontiers Media SA} } +@article{piersanti2023, + title = {Are brain displacements and pressures within the parenchyma induced by surface pressure differences? A computational modelling study}, + author = {Piersanti, Eleonora and Rognes, Marie E. and Vinje, Vegard}, + journal = {PLOS ONE}, + volume = {18}, + number = {5}, + pages = {e0288668}, + year = {2023}, + publisher = {Public Library of Science}, + doi = {10.1371/journal.pone.0288668} +} @unpublished{poulain2022, title = {{Multi-compartmental model of glymphatic clearance of solutes in brain tissue}}, author = {Poulain, Alexandre and Riseth, J{{\o}}rgen and Vinje, Vegard}, @@ -205,6 +244,15 @@ @unpublished{poulain2022 hal_id = {hal-03789563}, hal_version = {v1} } +@article{riseth2025human, + title = {Human brain MRI data of CSF tracer evolution over 72h for data-integrated simulations}, + author = {Riseth, J{\o}rgen N and Koch, Timo and Lian, Sofie Lysholm and Stor{\aa}s, Tryggve Holck and Zikatanov, Ludmil T and Valnes, Lars Magnus and Nordengen, Kaja and Mardal, Kent-Andr{\'e}}, + journal = {medRxiv}, + pages = {2025--07}, + year = {2025}, + publisher = {Cold Spring Harbor Laboratory Press}, + doi = {10.1101/2025.07.23.25331971} +} @article{saetra2021, doi = {10.1371/journal.pcbi.1008143}, author = {S\ae{}tra, Marte J. AND Einevoll, Gaute T. AND Halnes, Geir}, @@ -254,6 +302,17 @@ @inbook{valnes2022 isbn = {978-3-030-95136-8}, doi = {10.1007/978-3-030-95136-8_3} } +@article{vinje2023human, + title = {Human brain solute transport quantified by glymphatic MRI-informed biophysics during sleep and sleep deprivation}, + author = {Vinje, Vegard and Zapf, Bastian and Ringstad, Geir and Eide, Per Kristian and Rognes, Marie E and Mardal, Kent-Andre}, + journal = {Fluids and Barriers of the CNS}, + volume = {20}, + number = {1}, + pages = {62}, + year = {2023}, + publisher = {Springer}, + doi = {10.1186/s12987-023-00459-8} +} @misc{zapf2023medical, title = {Medical image registration using optimal control of a linear hyperbolic transport equation with a DG discretization}, author = {Bastian Zapf and Johannes Haubner and Lukas Baumg\"{a}rtner and Stephan Schmidt}, diff --git a/docs/repositories.md b/docs/repositories.md index abb72e5..01d251e 100644 --- a/docs/repositories.md +++ b/docs/repositories.md @@ -2,12 +2,16 @@ A list of repositories used in research in the Scientific Computing Department follows. A link to relevant publications/preprints is referenced. ## 2025 +- [In-silico molecular enrichment and clearance of the human intracranial space](https://github.com/MariusCausemann/brain-PVS-SAS-transport) {cite}`causemann2025insilico` +- [Advection versus diffusion in brain ventricular transport](https://github.com/hherlyng/zebrafish-cilia-csf) {cite}`herlyng2025advection` +- [Stretch and flow at the gliovascular interface: high-fidelity modelling of the mechanics of astrocyte endfeet](https://github.com/MariusCausemann/endfoot-mechanics) {cite}`causemann2025stretch` - [Impact of segregation scheme on performance of a strongly coupled cardiac electromechanical solver](https://github.com/ComputationalPhysiology/simcardems2) {cite}`MYKLEBUST2025118270` - [A software benchmark for cardiac elastodynamics](https://github.com/finsberg/cardiac_benchmark) {cite}`arostica2025117485` - [Arrhythmic Mitral Valve Syndrome: Insights from Left Ventricular End-Systolic Shape Analysis](https://github.com/ComputationalPhysiology/MAD-SSA) {cite}`monopoli2025arrhythmic` - [DeepValve: an automatic detection pipeline for the mitral valve in cardiac magnetic resonance imaging](https://github.com/giuliamonopoli/deepvalve-paper) {cite}`monopoli2025deepvalve` ## 2024 +- [Human brain MRI data of CSF tracer evolution over 72h for data-integrated simulations](https://github.com/jorgenriseth/gonzo) {cite}`riseth2025human` - [The sodium/glucose cotransporter 2 inhibitor Empagliflozin inhibits long QT 3 late sodium currents in a mutation specific manner](https://github.com/andygedwards/LQT3-SGLT2i) {cite}`LUNSONGA202599` - [An electrodiffusive network model with multicompartmental neurons and synaptic connections](https://github.com/martejulie/electrodiffusive-network-model) {cite}`saetra2024` - [Automatic motion estimation with applications to hiPSC-CMs](https://github.com/ComputationalPhysiology/automatic-motion-estimation) {cite}`10.1088/2057-1976/ad7268` @@ -15,7 +19,7 @@ A list of repositories used in research in the Scientific Computing Department f ## 2023 - +- [Human brain solute transport quantified by glymphatic MRI-informed biophysics during sleep and sleep deprivation](https://github.com/bzapf/braintransport) {cite}`vinje2023human` - [Medical image registration using optimal control of a linear hyperbolic transport equation with a DG discretization](https://github.com/JohannesHaubner/mapMRI) {cite}`zapf2023medical` - [ffian: Fluid Flow In Astrocyte Networks](https://github.com/martejulie/fluid-flow-in-astrocyte-networks) {cite}`sætra2023` - [A novel density based approach for topology optimization of Stokes flow](https://github.com/JohannesHaubner/TopOpt) {cite}`haubner2023` diff --git a/docs/resources.md b/docs/resources.md index f7341a0..9ba7b58 100644 --- a/docs/resources.md +++ b/docs/resources.md @@ -2,7 +2,7 @@ There are a few very good online guides on reproducible research. -- [The Turing way](https://the-turing-way.netlify.app/welcome.html) from the [Alan Turing institute](https://github.com/alan-turing-institute). This page contains information and guidelines about most of the things you need to know about reproducible research and we encourage everyone to skim through this site. They also have a [template repo](https://github.com/alan-turing-institute/reproducible-project-template) that might be relevant. +- [The Turing way](https://book.the-turing-way.org) from the [Alan Turing institute](https://github.com/alan-turing-institute). This page contains information and guidelines about most of the things you need to know about reproducible research and we encourage everyone to skim through this site. They also have a [template repo](https://github.com/alan-turing-institute/reproducible-project-template) that might be relevant. - [Scientific Python](https://learn.scientific-python.org/development/) is a guide on how to develop scientific software in Python. This guide is a bit more technical than the Turing way and is more focused on the software development part.