Merge pull request #60 from scientificcomputing/more-content

More content

Author: finsberg

.cspell_dict.txt

@@ -1,5 +1,6 @@
 addopts
 annefou
+arostica
 Astrocyte
 Bippe
 brainpulse
@@ -9,32 +10,41 @@ checkpointing
 cibuildwheel
 conda
 Cookiecutter
+cotransporter
 Daversin
 discretization
 docname
 docnames
 Dokken
 DOLFINx
+elastodynamics
 electrodiffusive
+Empagliflozin
 ffian
 finsberg
 Finsberg
 Forsch
 Fouilloux
+geometriesx
 Gjerde
 glymphatic
+gotranx
 Graphnics
 Haubner
 howpublished
 htmlcov
+idealised
 importlib
 Ingeborg
 Jørgen
 jorgensd
 Jupyterbook
 jupytext
 Laughlin
+ldrb
+LUNSONGA
 Meep
+microphysiological
 minrk
 multicompartmental
 Multiphysics

.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:

.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

docs/myst.yml

@@ -64,7 +64,25 @@ project:
 
 site:
   template: book-theme
+  nav:
+    - title: Home
+      url: /index
+    - title: Software
+      url: /packages
+    - title: Papers with code
+      url: /repositories
+    - title: Resources
+      url: /resources
+    - 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
+    favicon: _static/favicon.ico
     logo: _static/logo.png
     logo_dark: _static/logo.png

docs/packages.md

@@ -2,13 +2,41 @@
 
 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)
+- `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}`
+
 
 ## Missing a package?
 

docs/references.bib

@@ -1,15 +1,31 @@
-# 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`
+- [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`
 - [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`
+
+## 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?
 

docs/repositories.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.