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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 pre-release software under active development. No packages automating installation of either BETSEE itself or BETSEE dependencies are currently provided. In particular, there currently exist no:

BETSEE is installable as follows:

  1. Under Ubuntu Linux 16.04 (Xenial Xerus) and newer, by downloading and running an automated command-line installer.

    1. Open a terminal. [1]

    2. Download and run the BETSE[E] installer.

      wget && source betsee_ubuntu_16_04.bash
  2. Under all other platforms, by manually installing BETSEE and BETSE via your preferred package manager.

    1. Install the unstable live version of BETSE.

    2. Install Qt 5.9. [2]

    3. Install the stable 5.9 branch of PySide2. [2]

    4. Open a terminal. [1]

    5. Clone the master branch of this repository.

      git clone
    6. Install BETSEE.

      cd betsee
      sudo python3 install

Needless to say, Ubuntu Linux is strongly recommended for use of this pre-release version.

[1](1, 2)

To open a POSIX-compatible terminal under:

  • Windows:
    1. Install Bash on Ubuntu on Windows.
    2. Open the Start menu.
    3. Open Bash on Ubuntu on Windows.
  • macOS:
    1. Open the Finder.
    2. Open the Applications folder.
    3. Open the Utilities folder.
    4. Open
  • Ubuntu Linux:
    1. Type Ctrl+Alt+t.
[2](1, 2)

Like BETSEE, PySide2 is pre-release software under active development. Unlike BETSEE, packages automating installation of both PySide2 itself and PySide2 dependencies (e.g., Qt) are available for various platforms – including:


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). [3] Frontiers in Bioengineering and Biotechnology, 4(55).

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

[3]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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