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Software

A list scientific software (and corresponding publication) developed by personnel in the Scientific Computing Department.

FEniCS

  • Scientific finite element toolbox scifem
  • ADIOS4DOLFINx: A framework for checkpointing in FEniCS ADIOS4DOLFINx {cite}dokken2024adios
  • Multi-point constraints with DOLFINx: DOLFINx_MPC

Simulation

  • SMART: Spatial Modeling Algorithms for Reactions and Transport smart {cite}laughlin2023smart
  • Network models for FEniCS: Graphnics
  • Software Components for Multiphysics Problems: HAZniCS {cite}budisa2022

Meshing

  • Surface Volume Meshing ToolKit: SVMTK {cite}valnes2022
  • Tool for creating idealised cardiac geometries and microstructure in FEniCS: cardiac-geometries
  • Tool for creating idealised cardiac geometries and microstructure in FEniCSx: cardiac-geometriesx
  • A collection of tools for manipulation of morphological features in patient-specific geometries morphMan
  • Generate meshes from UK Biobank atlas ukb-atlas

Fluid Dynamics

  • Next generation Open Source Navier Stokes solver using FEniCSx oasisx
  • A verified and validated Python/FEniCS-based CFD solver for moving domains OasisMove
  • A collection of tools for pre-processing, simulating, and post-processing vascular morphologies VaMPy

FSI

  • A collection of tools for pre-processing, simulating, and post-processing vascular fluid-structure-interaction problems VaSP
  • Monolithic Fluid-Structure Interaction (FSI) solver turtleFSI

Brain

  • Intracranial Pulsation: brainpulse {cite}causemann2022

Heart

  • Simula Cardiac ElectroMechanics Solver simcardems {cite}finsberg2023
  • Tools for working with microphysiological data mps
  • Library for tracking motion in cardiac mps data mps-motion
  • Library for extracting action potential features ap-features
  • Cardiac Circulation Models: circulation
  • pulse - Cardiac mechanics solver in FEniCSx and FEnICS
  • beat - Cardiac electrophysiology solver in FEniCSx and FEnICS
  • ldrb - Library for creating rule-based fiber orientations in FEniCSx and FEniCS

Other

  • General ODE translator gotranx {cite}finsberg2024
  • A tool for visualizing dependencies between different components of your ODE model modelgraph

Missing a package?

If you package is missing from the list, go to Add new package

:filter: docname in docnames