From 60a1fa2609d2a4675f87f38f94fa8a170f9a3544 Mon Sep 17 00:00:00 2001 From: Henrik Finsberg Date: Mon, 23 Dec 2024 18:57:30 +0100 Subject: [PATCH 1/2] Add more content --- .cspell_dict.txt | 6 + .github/ISSUE_TEMPLATE/package.yml | 9 + .pre-commit-config.yaml | 5 + docs/myst.yml | 16 ++ docs/packages.md | 35 +++- docs/references.bib | 325 +++++++++++++++-------------- docs/repositories.md | 11 +- 7 files changed, 245 insertions(+), 162 deletions(-) diff --git a/.cspell_dict.txt b/.cspell_dict.txt index f5cd5b5..f2e2a13 100644 --- a/.cspell_dict.txt +++ b/.cspell_dict.txt @@ -1,5 +1,6 @@ addopts annefou +arostica Astrocyte Bippe brainpulse @@ -15,18 +16,22 @@ docname docnames Dokken DOLFINx +elastodynamics electrodiffusive ffian finsberg Finsberg Forsch Fouilloux +geometriesx Gjerde glymphatic +gotranx Graphnics Haubner howpublished htmlcov +idealised importlib Ingeborg Jørgen @@ -35,6 +40,7 @@ Jupyterbook jupytext Laughlin Meep +microphysiological minrk multicompartmental Multiphysics diff --git a/.github/ISSUE_TEMPLATE/package.yml b/.github/ISSUE_TEMPLATE/package.yml index 35ffb31..ec86ed4 100644 --- a/.github/ISSUE_TEMPLATE/package.yml +++ b/.github/ISSUE_TEMPLATE/package.yml @@ -27,6 +27,15 @@ body: validations: required: true + - type: input + id: label + attributes: + label: Label + description: Add label (see https://scientificcomputing.github.io/packages.html for existing labels) + placeholder: Brain + validations: + required: true + - type: textarea id: bib attributes: diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 2c4d548..22fcb5a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,3 +11,8 @@ repos: hooks: - id: cspell files: docs/(.+).md|README.md + - repo: https://github.com/FlamingTempura/bibtex-tidy + rev: v1.14.0 # see changelog for latest version + hooks: + - id: bibtex-tidy + args: ['--sort', '--merge'] # any other settings diff --git a/docs/myst.yml b/docs/myst.yml index 9c657f6..574ce96 100644 --- a/docs/myst.yml +++ b/docs/myst.yml @@ -64,6 +64,22 @@ project: site: template: book-theme + nav: + - title: Home + url: /index + - title: Software + url: /packages + - title: Papers with code + url: /repositories + - title: Departments + children: + - title: ComPhy + url: https://www.simula.no/research/research-departments/computational-physiology + - title: SCAN + url: https://www.simula.no/research/research-departments/numerical-analysis-and-scientific-computing + - title: HPC + url: https://www.simula.no/research/research-departments/high-performance-computing + options: # favicon: favicon.ico logo: _static/logo.png diff --git a/docs/packages.md b/docs/packages.md index 96d7f39..a9a991e 100644 --- a/docs/packages.md +++ b/docs/packages.md @@ -2,13 +2,38 @@ A list scientific software (and corresponding publication) developed by personnel in the Scientific Computing Department. -- ADIOS4DOLFINx: A framework for checkpointing in FEniCS [ADIOS4DOLFINx](https://github.com/jorgensd/adios4dolfinx/) {cite}`Dokken2024adios` -- SMART: Spatial Modeling Algorithms for Reactions and Transport [smart](https://github.com/RangamaniLabUCSD/smart) {cite}`Laughlin2023smart` -- Surface Volume Meshing ToolKit: [SVMTK](https://github.com/SVMTK/SVMTK) {cite}`Valnes2022` -- Intracranial Pulsation: [brainpulse](https://github.com/MariusCausemann/intracranialPulsation) {cite}`Causemann2022` -- Software Components for Multiphysics Problems: [HAZniCS](https://github.com/HAZmathTeam/hazmath) {cite}`budisa2022` + +## FEniCS +- ADIOS4DOLFINx: A framework for checkpointing in FEniCS [ADIOS4DOLFINx](https://github.com/jorgensd/adios4dolfinx/) {cite}`dokken2024adios` - Multi-point constraints with DOLFINx: [DOLFINx_MPC](https://github.com/jorgensd/dolfinx_mpc) + +## Simulation +- SMART: Spatial Modeling Algorithms for Reactions and Transport [smart](https://github.com/RangamaniLabUCSD/smart) {cite}`laughlin2023smart` - Network models for FEniCS: [Graphnics](https://github.com/IngeborgGjerde/graphnics) +- Software Components for Multiphysics Problems: [HAZniCS](https://github.com/HAZmathTeam/hazmath) {cite}`budisa2022` + +## Meshing +- Surface Volume Meshing ToolKit: [SVMTK](https://github.com/SVMTK/SVMTK) {cite}`valnes2022` +- Tool for creating idealised cardiac geometries and microstructure in FEniCS: [cardiac-geometries](https://github.com/ComputationalPhysiology/cardiac-geometries) +- Tool for creating idealised cardiac geometries and microstructure in FEniCSx: [cardiac-geometriesx](https://github.com/ComputationalPhysiology/cardiac-geometriesx) + + +## Fluid Dynamics +- Next generation Open Source Navier Stokes solver using FEniCSx [oasisx](https://github.com/ComputationalPhysiology/oasisx) + +## Brain +- Intracranial Pulsation: [brainpulse](https://github.com/MariusCausemann/intracranialPulsation) {cite}`causemann2022` + +## Heart +- Simula Cardiac ElectroMechanics Solver [simcardems](https://github.com/ComputationalPhysiology/simcardems) {cite}`finsberg2023` +- Tools for working with microphysiological data [mps](https://github.com/ComputationalPhysiology/mps) +- Library for tracking motion in cardiac mps data [mps-motion](https://github.com/ComputationalPhysiology/mps_motion) +- Library for extracting action potential features [ap-features](https://github.com/ComputationalPhysiology/ap_features) +- Cardiac Circulation Models: [circulation](https://github.com/ComputationalPhysiology/circulation) + +## Other +- General ODE translator [gotranx](https://github.com/finsberg/gotranx) {cite}` + ## Missing a package? diff --git a/docs/references.bib b/docs/references.bib index bb3d0a2..cd5cfd1 100644 --- a/docs/references.bib +++ b/docs/references.bib @@ -1,161 +1,182 @@ - +@article{10.1088/2057-1976/ad7268, + author = {Finsberg, Henrik Nicolay Topnes and Charwat, Verena and Healy, Kevin E and Wall, Samuel}, + title = {Automatic motion estimation with applications to hiPSC-CMs}, + journal = {Biomedical Physics \& Engineering Express}, + url = {http://iopscience.iop.org/article/10.1088/2057-1976/ad7268}, + year = {2024} +} +@article{arostica2025117485, + title = {A software benchmark for cardiac elastodynamics}, + journal = {Computer Methods in Applied Mechanics and Engineering}, + volume = {435}, + pages = {117485}, + year = {2025}, + issn = {0045-7825}, + doi = {https://doi.org/10.1016/j.cma.2024.117485}, + url = {https://www.sciencedirect.com/science/article/pii/S0045782524007394}, + author = {Reidmen Ar\'{o}stica and David Nolte and Aaron Brown and Amadeus Gebauer and Elias Karabelas and Javiera Jilberto and Matteo Salvador and Michele Bucelli and Roberto Piersanti and Kasra Osouli and Christoph Augustin and Henrik Finsberg and Lei Shi and Marc Hirschvogel and Martin Pfaller and Pasquale Claudio Africa and Matthias Gsell and Alison Marsden and David Nordsletten and Francesco Regazzoni and Gernot Plank and Joakim Sundnes and Luca Dede' and Mathias Peirlinck and Vijay Vedula and Wolfgang Wall and Crist\'{o}bal Bertoglio}, + keywords = {Cardiac mechanics, Software, Finite elements, Benchmark, Hyperelasticity}, + abstract = {In cardiovascular mechanics, reaching consensus in simulation results within a physiologically relevant range of parameters is essential for reproducibility purposes. Although currently available benchmarks contain some of the features that cardiac mechanics models typically include, some important modeling aspects are missing. Therefore, we propose a new set of cardiac benchmark problems and solutions for assessing passive and active material behavior, viscous effects, and pericardial boundary condition. The problems proposed include simplified analytical fiber definitions and active stress models on a monoventricular and biventricular domains, allowing straightforward testing and validation with already developed solvers.} +} +@misc{budisa2022, + doi = {10.48550/ARXIV.2210.13274}, + url = {https://arxiv.org/abs/2210.13274}, + author = {Budisa, Ana and Hu, Xiaozhe and Kuchta, Miroslav and Mardal, Kent-Andre and Zikatanov, Ludmil}, + keywords = {Numerical Analysis (math.NA), FOS: Mathematics, FOS: Mathematics, G.1.8; G.4, 65-04, 65N55, 65F08, 65H10}, + title = {{HAZniCS -- Software Components for Multiphysics Problems}}, + publisher = {arXiv}, + year = {2022}, + copyright = {arXiv.org perpetual, non-exclusive license} +} +@article{causemann2022, + author = {Causemann, Marius and Vinje, Vegard and Rognes, Marie E.}, + title = {Human intracranial pulsatility during the cardiac cycle: a computational modelling framework}, + elocation-id = {2022.05.19.492650}, + year = {2022}, + doi = {10.1101/2022.05.19.492650}, + publisher = {Cold Spring Harbor Laboratory}, + journal = {bioRxiv} +} +@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}}, + journal = {Frontiers in Physics}, + volume = {10}, + year = {2022}, + doi = {10.3389/fphy.2022.882260}, + issn = {2296-424X} +} +@article{dokken2024adios, + doi = {10.21105/joss.06451}, + year = {2024}, + publisher = {The Open Journal}, + volume = {9}, + number = {96}, + pages = {6451}, + author = {J\o{}rgen Schartum Dokken}, + title = {{ADIOS4DOLFINx: A framework for checkpointing in FEniCS}}, + journal = {Journal of Open Source Software} +} +@article{finsberg2023, + doi = {10.21105/joss.04753}, + url = {https://doi.org/10.21105/joss.04753}, + year = {2023}, + publisher = {The Open Journal}, + volume = {8}, + number = {81}, + pages = {4753}, + author = {Henrik Nicolay Topnes Finsberg and Ilsbeth Gerarda Maria van Herck and C\'{e}cile Daversin-Catty and Hermenegild Arevalo and Samuel Wall}, + title = {simcardems: A FEniCS-based cardiac electro-mechanics solver}, + journal = {Journal of Open Source Software} +} +@article{finsberg2024, + doi = {10.21105/joss.07063}, + url = {https://doi.org/10.21105/joss.07063}, + year = {2024}, + publisher = {The Open Journal}, + volume = {9}, + number = {102}, + pages = {7063}, + author = {Henrik Finsberg and Johan Hake}, + title = {gotranx: General ODE translator}, + journal = {Journal of Open Source Software} +} +@article{gjerde2022, + title = {Nitsche's method for Navier--Stokes equations with slip boundary conditions}, + author = {Gjerde, Ingeborg and Scott, L}, + journal = {Mathematics of Computation}, + volume = {91}, + number = {334}, + pages = {597--622}, + year = {2022}, + doi = {10.1090/mcom/3682} +} +@article{haubner2021, + author = {Haubner, Johannes and Neumann, Franziska and Ulbrich, Michael}, + title = {{A Novel Density Based Approach for Topology Optimization of Stokes Flow}}, + journal = {SIAM Journal on Scientific Computing}, + volume = {45}, + number = {2}, + pages = {A338-A368}, + year = {2023}, + doi = {10.1137/21M143114X} +} +@article{laughlin2023smart, + doi = {10.21105/joss.05580}, + year = {2023}, + publisher = {The Open Journal}, + volume = {8}, + number = {90}, + pages = {5580}, + author = {Justin G. Laughlin and J\o{}rgen S. Dokken and Henrik N.t. Finsberg and Emmet A. Francis and Christopher T. Lee and Marie E. Rognes and Padmini Rangamani}, + title = {{SMART: Spatial Modeling Algorithms for Reactions and Transport}}, + journal = {Journal of Open Source Software} +} @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}, - url = {https://hal.archives-ouvertes.fr/hal-03789563}, - note = {working paper or preprint}, - year = {2022}, - month = Sep, - pdf = {https://hal.archives-ouvertes.fr/hal-03789563/file/multicompartment-glymphatics.pdf}, - hal_id = {hal-03789563}, - hal_version = {v1} -} - - -@article{Causemann2022, - author = {Causemann, Marius and Vinje, Vegard and Rognes, Marie E.}, - title = {Human intracranial pulsatility during the cardiac cycle: a computational modelling framework}, - elocation-id = {2022.05.19.492650}, - year = {2022}, - doi = {10.1101/2022.05.19.492650}, - publisher = {Cold Spring Harbor Laboratory}, - journal = {bioRxiv} -} - - -@inbook{Valnes2022, - author = {Mardal, Kent-Andr{\'e} - and Rognes, Marie E. - and Thompson, Travis B. - and Valnes, Lars Magnus}, - title = {{Getting started: from T1 images to simulation}}, - booktitle = {{Mathematical Modeling of the Human Brain: From Magnetic Resonance Images to Finite Element Simulation}}, - year = {2022}, - publisher = {{Springer International Publishing}}, - address = {Cham}, - pages = {23--46}, - isbn = {978-3-030-95136-8}, - doi = {10.1007/978-3-030-95136-8_3} -} - - -@article{Daversin2022, - author = {Daversin-Catty, Cécile and Gjerde, Ingeborg G. and Rognes, Marie E.}, - title = {{Geometrically Reduced Modelling of Pulsatile Flow in Perivascular Networks}}, - journal = {Frontiers in Physics}, - volume = {10}, - year = {2022}, - doi = {10.3389/fphy.2022.882260}, - issn = {2296-424X} -} - - -@article{Gjerde2022, - title = {Nitsche's method for Navier--Stokes equations with slip boundary conditions}, - author = {Gjerde, Ingeborg and Scott, L}, - journal = {Mathematics of Computation}, - volume = {91}, - number = {334}, - pages = {597--622}, - year = {2022}, - doi = {10.1090/mcom/3682} -} - - -@article{Haubner2021, - author = {Haubner, Johannes and Neumann, Franziska and Ulbrich, Michael}, - title = {{A Novel Density Based Approach for Topology Optimization of Stokes Flow}}, - journal = {SIAM Journal on Scientific Computing}, - volume = {45}, - number = {2}, - pages = {A338-A368}, - year = {2023}, - doi = {10.1137/21M143114X} -} - + title = {{Multi-compartmental model of glymphatic clearance of solutes in brain tissue}}, + author = {Poulain, Alexandre and Riseth, J{{\o}}rgen and Vinje, Vegard}, + url = {https://hal.archives-ouvertes.fr/hal-03789563}, + note = {working paper or preprint}, + year = {2022}, + month = sep, + pdf = {https://hal.archives-ouvertes.fr/hal-03789563/file/multicompartment-glymphatics.pdf}, + hal_id = {hal-03789563}, + hal_version = {v1} +} @article{saetra2021, - doi = {10.1371/journal.pcbi.1008143}, - author = {Sætra, Marte J. AND Einevoll, Gaute T. AND Halnes, Geir}, - journal = {PLOS Computational Biology}, - publisher = {Public Library of Science}, - title = {An electrodiffusive neuron-extracellular-glia model for exploring the genesis of slow potentials in the brain}, - year = {2021}, - month = {07}, - volume = {17}, - pages = {1-45}, - number = {7} -} - -@misc{budisa2022, - doi = {10.48550/ARXIV.2210.13274}, - url = {https://arxiv.org/abs/2210.13274}, - author = {Budisa, Ana and Hu, Xiaozhe and Kuchta, Miroslav and Mardal, Kent-Andre and Zikatanov, Ludmil}, - keywords = {Numerical Analysis (math.NA), FOS: Mathematics, FOS: Mathematics, G.1.8; G.4, 65-04, 65N55, 65F08, 65H10}, - title = {{HAZniCS -- Software Components for Multiphysics Problems}}, - publisher = {arXiv}, - year = {2022}, - copyright = {arXiv.org perpetual, non-exclusive license} -} - + doi = {10.1371/journal.pcbi.1008143}, + author = {S\ae{}tra, Marte J. AND Einevoll, Gaute T. AND Halnes, Geir}, + journal = {PLOS Computational Biology}, + publisher = {Public Library of Science}, + title = {An electrodiffusive neuron-extracellular-glia model for exploring the genesis of slow potentials in the brain}, + year = {2021}, + month = {07}, + volume = {17}, + pages = {1--45}, + number = {7} +} +@article{sætra2023, + doi = {10.1371/journal.pcbi.1010996}, + author = {S\ae{}tra, Marte J. AND Ellingsrud, Ada J. AND Rognes, Marie E.}, + journal = {PLOS Computational Biology}, + publisher = {Public Library of Science}, + title = {Neural activity induces strongly coupled electro-chemo-mechanical interactions and fluid flow in astrocyte networks and extracellular space--A computational study}, + year = {2023}, + month = {07}, + volume = {19}, + url = {https://doi.org/10.1371/journal.pcbi.1010996}, + pages = {1--31}, + number = {7} +} +@article{saetra2024, + doi = {10.1371/journal.pcbi.1012114}, + author = {S\ae{}tra, Marte J. AND Mori, Yoichiro}, + journal = {PLOS Computational Biology}, + publisher = {Public Library of Science}, + title = {An electrodiffusive network model with multicompartmental neurons and synaptic connections}, + year = {2024}, + month = {11}, + volume = {20}, + url = {https://doi.org/10.1371/journal.pcbi.1012114}, + pages = {1--33}, + number = {11} +} +@inbook{valnes2022, + author = {Mardal, Kent-Andr{\'e} and Rognes, Marie E. and Thompson, Travis B. and Valnes, Lars Magnus}, + title = {{Getting started: from T1 images to simulation}}, + booktitle = {{Mathematical Modeling of the Human Brain: From Magnetic Resonance Images to Finite Element Simulation}}, + year = {2022}, + publisher = {{Springer International Publishing}}, + address = {Cham}, + pages = {23--46}, + isbn = {978-3-030-95136-8}, + doi = {10.1007/978-3-030-95136-8_3} +} @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 Baumgärtner and Stephan Schmidt}, + author = {Bastian Zapf and Johannes Haubner and Lukas Baumg\"{a}rtner and Stephan Schmidt}, year = {2023}, eprint = {2305.03020}, archiveprefix = {arXiv}, primaryclass = {math.NA} } - - -@article{Dokken2024adios, - doi = {10.21105/joss.06451}, - year = {2024}, - publisher = {The Open Journal}, - volume = {9}, - number = {96}, - pages = {6451}, - author = {Jørgen Schartum Dokken}, - title = {{ADIOS4DOLFINx: A framework for checkpointing in FEniCS}}, - journal = {Journal of Open Source Software} -} - - -@article{Laughlin2023smart, - doi = {10.21105/joss.05580}, - year = {2023}, - publisher = {The Open Journal}, - volume = {8}, - number = {90}, - pages = {5580}, - author = {Justin G. Laughlin and Jørgen S. Dokken and Henrik N.t. Finsberg and Emmet A. Francis and Christopher T. Lee and Marie E. Rognes and Padmini Rangamani}, - title = {{SMART: Spatial Modeling Algorithms for Reactions and Transport}}, - journal = {Journal of Open Source Software} -} - -@article{Sætra2023, - doi = {10.1371/journal.pcbi.1010996}, - author = {Sætra, Marte J. AND Ellingsrud, Ada J. AND Rognes, Marie E.}, - journal = {PLOS Computational Biology}, - publisher = {Public Library of Science}, - title = {Neural activity induces strongly coupled electro-chemo-mechanical interactions and fluid flow in astrocyte networks and extracellular space—A computational study}, - year = {2023}, - month = {07}, - volume = {19}, - url = {https://doi.org/10.1371/journal.pcbi.1010996}, - pages = {1-31}, - number = {7} -} - -@article{saetra2024, - doi = {10.1371/journal.pcbi.1012114}, - author = {Sætra, Marte J. AND Mori, Yoichiro}, - journal = {PLOS Computational Biology}, - publisher = {Public Library of Science}, - title = {An electrodiffusive network model with multicompartmental neurons and synaptic connections}, - year = {2024}, - month = {11}, - volume = {20}, - url = {https://doi.org/10.1371/journal.pcbi.1012114}, - pages = {1-33}, - number = {11} -} diff --git a/docs/repositories.md b/docs/repositories.md index 6113e6f..de73828 100644 --- a/docs/repositories.md +++ b/docs/repositories.md @@ -2,15 +2,16 @@ A list of repositories used in research in the Scientific Computing Department follows. A link to relevant publications/preprints is referenced. - [Multi-compartmental model of glymphatic clearance of solutes in brain tissue](https://github.com/jorgenriseth/multicompartment-solute-transport) {cite}`poulain2022` -- [Geometrically reduced modelling of pulsatile flow in perivascular networks](https://github.com/cdaversin/geometrically-reduced-PVS-flow) {cite}`Daversin2022` -- [Nitsche method for solving Navier-Stokes with slip boundary conditions](https://github.com/IngeborgGjerde/nitsche-method-for-navier-stokes-with-slip) {cite}`Gjerde2022` -- [A novel density based approach for topology optimization of Stokes flow](https://github.com/JohannesHaubner/TopOpt) {cite}`Haubner2021` +- [Geometrically reduced modelling of pulsatile flow in perivascular networks](https://github.com/cdaversin/geometrically-reduced-PVS-flow) {cite}`daversin2022` +- [Nitsche method for solving Navier-Stokes with slip boundary conditions](https://github.com/IngeborgGjerde/nitsche-method-for-navier-stokes-with-slip) {cite}`gjerde2022` +- [A novel density based approach for topology optimization of Stokes flow](https://github.com/JohannesHaubner/TopOpt) {cite}`haubner2021` - [An electrodiffusive neuron-extracellular-glia model for exploring the genesis of slow potentials in the brain](https://github.com/CINPLA/edNEGmodel_analysis) {cite}`saetra2021` - [HAZniCS - Software Components for Multiphysics Problems](https://github.com/anabudisa/HAZniCS-examples) {cite}`budisa2022` - [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` +- [ffian: Fluid Flow In Astrocyte Networks](https://github.com/martejulie/fluid-flow-in-astrocyte-networks) {cite}`sætra2023` - [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} +- [A software benchmark for cardiac elastodynamics](https://github.com/finsberg/cardiac_benchmark) {cite}`arostica2025117485` ## Missing a repository? If you repository is missing from the list, go to [Add new repository](https://github.com/scientificcomputing/scientificcomputing.github.io/issues/new?assignees=&labels=new-repo&template=repository.yml&title=%5BAdd+repo%5D%3A+) From 334ad51c0d8e5d25caaee62fad084428e84f2957 Mon Sep 17 00:00:00 2001 From: Henrik Finsberg Date: Mon, 23 Dec 2024 21:44:34 +0100 Subject: [PATCH 2/2] Add more content --- .cspell_dict.txt | 4 ++++ docs/myst.yml | 4 +++- docs/packages.md | 3 +++ docs/references.bib | 15 ++++++++++++++- docs/repositories.md | 31 +++++++++++++++++++++++-------- docs/resources.md | 12 +++++++++--- 6 files changed, 56 insertions(+), 13 deletions(-) diff --git a/.cspell_dict.txt b/.cspell_dict.txt index f2e2a13..31dfe43 100644 --- a/.cspell_dict.txt +++ b/.cspell_dict.txt @@ -10,6 +10,7 @@ checkpointing cibuildwheel conda Cookiecutter +cotransporter Daversin discretization docname @@ -18,6 +19,7 @@ Dokken DOLFINx elastodynamics electrodiffusive +Empagliflozin ffian finsberg Finsberg @@ -39,6 +41,8 @@ jorgensd Jupyterbook jupytext Laughlin +ldrb +LUNSONGA Meep microphysiological minrk diff --git a/docs/myst.yml b/docs/myst.yml index 574ce96..25c2205 100644 --- a/docs/myst.yml +++ b/docs/myst.yml @@ -71,6 +71,8 @@ site: url: /packages - title: Papers with code url: /repositories + - title: Resources + url: /resources - title: Departments children: - title: ComPhy @@ -81,6 +83,6 @@ site: url: https://www.simula.no/research/research-departments/high-performance-computing options: - # favicon: favicon.ico + favicon: _static/favicon.ico logo: _static/logo.png logo_dark: _static/logo.png diff --git a/docs/packages.md b/docs/packages.md index a9a991e..e914321 100644 --- a/docs/packages.md +++ b/docs/packages.md @@ -30,6 +30,9 @@ A list scientific software (and corresponding publication) developed by personne - Library for tracking motion in cardiac mps data [mps-motion](https://github.com/ComputationalPhysiology/mps_motion) - Library for extracting action potential features [ap-features](https://github.com/ComputationalPhysiology/ap_features) - Cardiac Circulation Models: [circulation](https://github.com/ComputationalPhysiology/circulation) +- `pulse` - Cardiac mechanics solver in [FEniCSx](https://github.com/finsberg/fenicsx-pulse) and [FEnICS](https://github.com/finsberg/pulse) +- `beat` - Cardiac electrophysiology solver in [FEniCSx](https://github.com/finsberg/fenicsx-beat) and [FEnICS](https://github.com/finsberg/fenics-beat) +- `ldrb` - Library for creating rule-based fiber orientations in [FEniCSx](https://github.com/finsberg/fenicsx-ldrb) and [FEniCS](https://github.com/finsberg/ldrb) ## Other - General ODE translator [gotranx](https://github.com/finsberg/gotranx) {cite}` diff --git a/docs/references.bib b/docs/references.bib index cd5cfd1..99b6632 100644 --- a/docs/references.bib +++ b/docs/references.bib @@ -91,7 +91,7 @@ @article{gjerde2022 year = {2022}, doi = {10.1090/mcom/3682} } -@article{haubner2021, +@article{haubner2023, author = {Haubner, Johannes and Neumann, Franziska and Ulbrich, Michael}, title = {{A Novel Density Based Approach for Topology Optimization of Stokes Flow}}, journal = {SIAM Journal on Scientific Computing}, @@ -112,6 +112,19 @@ @article{laughlin2023smart title = {{SMART: Spatial Modeling Algorithms for Reactions and Transport}}, journal = {Journal of Open Source Software} } +@article{LUNSONGA202599, + title = {The sodium/glucose cotransporter 2 inhibitor Empagliflozin inhibits long QT 3 late sodium currents in a mutation specific manner}, + journal = {Journal of Molecular and Cellular Cardiology}, + volume = {198}, + pages = {99--111}, + year = {2025}, + issn = {0022-2828}, + doi = {https://doi.org/10.1016/j.yjmcc.2024.11.014}, + url = {https://www.sciencedirect.com/science/article/pii/S0022282824002049}, + author = {Lynn C. Lunsonga and Mohammad Fatehi and Wentong Long and Amy J. Barr and Brittany Gruber and Arkapravo Chattopadhyay and Khaled Barakat and Andrew G. Edwards and Peter E. Light}, + keywords = {Empagliflozin, Long QT syndrome type 3, Late sodium current, Nav1.5, Arrhythmia, Cardioprotection}, + abstract = {Background Sodium/glucose cotransporter 2 inhibitors (SGLT2is) like empagliflozin have demonstrated cardioprotective effects in patients with or without diabetes. SGLT2is have been shown to selectively inhibit the late component of cardiac sodium current (late INa). Induction of late INa is the primary mechanism in the pathophysiology of congenital long QT syndrome type 3 (LQT3) gain-of-function mutations in the SCN5A gene encoding Nav1.5. We investigated empagliflozin's effect on late INa in thirteen known LQT3 mutations located in distinct regions of the channel. Methods The whole-cell patch-clamp technique was used to investigate the effect of empagliflozin on late INa in recombinantly expressed Nav1.5 channels containing different LQT3 mutations. Molecular modeling of human Nav1.5 and simulations in a mathematical model of human ventricular myocytes were used to extrapolate our experimental results to excitation-contraction coupling. Results Empagliflozin selectively inhibited late INa in LQT3 mutations in the inactivation gate region of Nav1.5, without affecting peak current or channel kinetics. In contrast, empagliflozin inhibited both peak and late INa in mutations in the S4 voltage-sensing regions, altered channel gating, and slowed recovery from inactivation. Empagliflozin had no effect on late/peak INa or channel kinetics in channels with mutations in the putative empagliflozin binding region. Simulation results predict that empagliflozin may have a desirable therapeutic effect in LQT3 mutations in the inactivation gate region. Conclusions Empagliflozin selectively inhibits late INa, without affecting channel kinetics, in LQT3 mutations in the inactivation gate region. Empagliflozin may thus be a promising precision medicine approach for patients with specific LQT3 mutations.} +} @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}, diff --git a/docs/repositories.md b/docs/repositories.md index de73828..b49fb54 100644 --- a/docs/repositories.md +++ b/docs/repositories.md @@ -1,17 +1,32 @@ -# Repositories +# Papers with code A list of repositories used in research in the Scientific Computing Department follows. A link to relevant publications/preprints is referenced. + +## 2024 +- [A software benchmark for cardiac elastodynamics](https://github.com/finsberg/cardiac_benchmark) {cite}`arostica2025117485` +- [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` + + +## 2023 + +- [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` + + +## 2022 - [Multi-compartmental model of glymphatic clearance of solutes in brain tissue](https://github.com/jorgenriseth/multicompartment-solute-transport) {cite}`poulain2022` - [Geometrically reduced modelling of pulsatile flow in perivascular networks](https://github.com/cdaversin/geometrically-reduced-PVS-flow) {cite}`daversin2022` - [Nitsche method for solving Navier-Stokes with slip boundary conditions](https://github.com/IngeborgGjerde/nitsche-method-for-navier-stokes-with-slip) {cite}`gjerde2022` -- [A novel density based approach for topology optimization of Stokes flow](https://github.com/JohannesHaubner/TopOpt) {cite}`haubner2021` -- [An electrodiffusive neuron-extracellular-glia model for exploring the genesis of slow potentials in the brain](https://github.com/CINPLA/edNEGmodel_analysis) {cite}`saetra2021` - [HAZniCS - Software Components for Multiphysics Problems](https://github.com/anabudisa/HAZniCS-examples) {cite}`budisa2022` -- [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` -- [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} -- [A software benchmark for cardiac elastodynamics](https://github.com/finsberg/cardiac_benchmark) {cite}`arostica2025117485` + +## 2021 +- [An electrodiffusive neuron-extracellular-glia model for exploring the genesis of slow potentials in the brain](https://github.com/CINPLA/edNEGmodel_analysis) {cite}`saetra2021` + + + ## Missing a repository? If you repository is missing from the list, go to [Add new repository](https://github.com/scientificcomputing/scientificcomputing.github.io/issues/new?assignees=&labels=new-repo&template=repository.yml&title=%5BAdd+repo%5D%3A+) diff --git a/docs/resources.md b/docs/resources.md index 425a926..2076847 100644 --- a/docs/resources.md +++ b/docs/resources.md @@ -1,9 +1,15 @@ -# Other Resources +# Resources There are a few very good online guides on reproducible research. -Perhaps the most comprehensive one is [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://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. -Another relevant project is [Papers with code](https://github.com/paperswithcode) which is probably more targeted machine learning projects. The also have a pretty comprehensive guide at https://github.com/paperswithcode/releasing-research-code. +- [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. + +- [CodeRefinery](https://coderefinery.org/) is a project that aims to teach researchers how to write better code. They have a lot of good resources and workshops that you can attend. + +- [Sigma2 training](https://www.sigma2.no/training-and-events) is a Norwegian project that provides training in high performance computing and data management. They have links to a lot of good resources. + +- [Papers with code](https://github.com/paperswithcode) which is probably more targeted machine learning projects. The also have a pretty comprehensive guide at https://github.com/paperswithcode/releasing-research-code. Getting inspiration from other project is often a good way. Papers with code also has a [web page](https://paperswithcode.com) where you can search for papers with code. For example you, could try to [search for FEniCS](https://paperswithcode.com/search?q_meta=&q_type=&q=FEniCS) and you will get a list of projects where FEniCS is mentioned.