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BETSEE, the BioElectric Tissue Simulation Engine Environment.

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BETSEE (BioElectric Tissue Simulation Engine Environment) is the open-source cross-platform graphical user interface (GUI) for BETSE, a finite volume simulator for 2D computational multiphysics problems in the life sciences – including electrodiffusion, electro-osmosis, galvanotaxis, voltage-gated ion channels, gene regulatory networks, and biochemical reaction networks (e.g., metabolism).

Like BETSE, BETSEE is portably implemented in pure Python 3, continuously stress-tested with GitLab-CI × Appveyor + py.test, and permissively distributed under the BSD 2-clause license.

BETSEE and BETSE are both associated with the Paul Allen Discovery Center at Tufts University and supported by a Paul Allen Discovery Center award from the Paul G. Allen Frontiers Group.


BETSEE is installable under Linux, macOS, and Windows as follows:

[1]The Windows Subsystem for Linux (WSL) and – hence BETSEE itself – is only installable under Windows 10. Under older Windows versions, BETSEE may be installed from a virtual Linux guest.
[2]Do not install the Python 2.7 variant of Anaconda. BETSEE requires Python 3.x.
[3]BETSEE is currently only installable via Anaconda, a cross-platform scientific Python distribution simplifying installation of non-Python dependencies (e.g., OpenBLAS, PySide2). While a PyPI package for installing BETSEE under pip (the standard Python package manager) does exist, that package is currently uninstallable due to a lack of official PySide2 wheels. Even when official PySide2 wheels are published, Anaconda will remain the official installation path for BETSE and hence BETSEE. pip commonly produces a performance-crippled single-core installation of BETSE. Anaconda suffers no such issues and is guaranteed to produce a performance-optimized multicore installation of BETSE on all supported platforms. We strongly recommend Anaconda – even when you think you know better.

To open a POSIX-compatible terminal under:

  • Windows:
    1. Install Ubuntu Linux via the Windows Subsystem for Linux (WSL).
    2. Open an Ubuntu Linux terminal.
  • macOS:
    1. Open the Finder.
    2. Open the Applications folder.
    3. Open the Utilities folder.
    4. Open
  • Ubuntu Linux:
    1. Type Ctrl+Alt+t.
[5]This command installs both the most recent stable release of BETSEE and all mandatory and most optional dependencies of this release. Older stable releases are installable in a similar manner (e.g., conda install betsee=0.8.2 for BETSEE 0.8.2). All Anaconda packages are kindly hosted by the non-profit conda-forge organization.


BETSEE is open-source software released under the permissive BSD 2-clause license. BETSEE contains third-party assets also released under BSD-compatible licenses, including:


BETSE is formally described in our introductory paper. Third-party papers, theses, and other texts leveraging BETSEE (and hence BETSE) should ideally cite the following:

Alexis Pietak and Michael Levin, 2016. Exploring instructive physiological signaling with the bioelectric tissue simulation engine (BETSE). (Supplement). [6] Frontiers in Bioengineering and Biotechnology, 4(55).

See also this list of BETSE-centric papers for additional material.

[6]This article’s supplement extends the cursory theory presented by this article with a rigorous treatment of the mathematics, formalisms, and abstractions required to fully reproduce this work. If theoretical questions remain after completing the main article, please consult this supplement.


BETSEE comes courtesy a dedicated community of authors and contributors – without whom this project would be computationally impoverished, biologically misaligned, and simply unusable.

Thanks, all.

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