Freedom251 › Physics Simulation Software
FEniCSx-beat
What FEniCSx-beat is
FEniCSx-beat is free MIT-licensed desktop software for researchers running cardiac electrophysiology simulations with FEniCSx. Its API provides Monodomain and Bidomain models, while the project centers on Monodomain simulations. The `beat` command-line tool runs tissue-level simulations and postprocessing from a `config.toml` file. For high-performance computing, it supports parameter-sweep array jobs and restarting a long run after a wall-time limit, including on another node allocation. The documented workflow uses FEniCSx components such as DOLFINx and UFL, with MPI through mpi4py in an example. Demonstrations include cardiac cell models, conduction-velocity and pseudo-ECG estimation, and recovery of a 12-lead ECG in a biventricular example. Installation is available with pip or conda; pip requires FEniCSx first. CLI dependencies come through the `cli` extra, while most examples need `fenicsx-beat[demos]`. Visualization with `beat post` additionally requires PyVista. Irksome solver configurations require the project’s Irksome extra.
Who it suits
It suits researchers using FEniCSx for cardiac electrophysiology and tissue simulations. Users working on HPC workflows, ECG estimation, or documented demonstration models may find its command-line tools relevant.
What it does well
- Free MIT-licensed desktop software
- Includes Monodomain and Bidomain APIs
- Supports parameter-sweep HPC array jobs
- Can restart runs after wall-time limits
- Provides ECG and conduction demonstrations
What to know first
- Pip installation requires FEniCSx first
- Examples often need an additional demos extra
- Postprocessing visualization requires PyVista
- Some CLI capabilities remain future work
Verdict
FEniCSx-beat offers a focused simulation workflow for FEniCSx-based cardiac research, including HPC job handling and ECG-related examples. Installation extras and documented CLI limitations should be considered before adopting it.
Facts from FEniCSx-beat's own pages
- Assessment tools
- No · finsberg.github.io, 24 Sept 2026
- Authoring tools
- No · finsberg.github.io, 24 Sept 2026
- Cell models
- The demos include cardiac cell-model simulations, including a ToRORd-based left-ventricle example with distinct endocardial, mid-myocardial, and epicardial parameterizations. · finsberg.github.io, 11 Oct 2026
- Citation
- The project requests citation of its 2025 Journal of Open Source Software paper when used in research. · finsberg.github.io, 11 Oct 2026
- CLI limitation
- The CLI documentation says per-region different `.ode` files and changing ODE parameters at specific times are future work. · finsberg.github.io, 11 Oct 2026
- CLI limits
- The CLI documentation says per-region separate `.ode` files and changing ODE parameters during a run are future work, and some demos are not yet fully reproducible through the CLI. · finsberg.github.io, 11 Oct 2026
- Command line
- The `beat` command line tool runs tissue-level Monodomain simulations and postprocessing from a `config.toml` file. · finsberg.github.io, 11 Oct 2026
- Delivery mode
- desktop · finsberg.github.io, 24 Sept 2026
- ECG
- The demos include conduction-velocity and pseudo-ECG estimation, as well as recovery of a 12-lead ECG in a biventricular example. · finsberg.github.io, 11 Oct 2026
- Ecosystem
- The documented workflow uses FEniCSx components including DOLFINx and UFL, and its example also uses MPI through mpi4py. · finsberg.github.io, 11 Oct 2026
- Examples
- The documentation says most examples need additional dependencies, available with the `fenicsx-beat[demos]` extra. · finsberg.github.io, 11 Oct 2026
- Free plan
- Yes · finsberg.github.io, 24 Sept 2026
- Help
- The project asks users with issues to submit a GitHub issue. · finsberg.github.io, 11 Oct 2026
- HPC workflow
- The CLI supports parameter-sweep array jobs and restarting a long run after a wall-time limit, potentially on a different node allocation. · finsberg.github.io, 11 Oct 2026
- Installation
- The library can be installed with pip or conda, and pip installation requires FEniCSx to be installed already. · finsberg.github.io, 11 Oct 2026
- Lesson library
- No · finsberg.github.io, 24 Sept 2026
- License
- The project README lists the software license as MIT. · finsberg.github.io, 11 Oct 2026
- Maker
- The README credits Henrik Finsberg as the documentation author and names him as the software paper's author. · finsberg.github.io, 11 Oct 2026
- Model
- The project describes simulations based on the Monodomain model. · finsberg.github.io, 11 Oct 2026
- Open source
- The project is distributed under the MIT license. · finsberg.github.io, 11 Oct 2026
- Optional dependencies
- CLI dependencies are provided through the `cli` extra, while visualization for `beat post` additionally requires PyVista. · finsberg.github.io, 11 Oct 2026
- Optional solver dependency
- Configs using the Irksome PDE or ODE solver require installing the `irksome` extra from the project's Git repository as described in the CLI documentation. · finsberg.github.io, 11 Oct 2026
- Postprocessing dependency
- CLI visualization with `beat post` additionally needs PyVista, which the documentation describes as optional. · finsberg.github.io, 11 Oct 2026
- Purpose
- FEniCSx-beat is a cardiac electrophysiology simulator for researchers using FEniCSx to run Monodomain simulations. · finsberg.github.io, 11 Oct 2026
Where FEniCSx-beat stands on Freedom251
- Physics Simulation Software#62 of 89