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BETSEE, the BioElectric Tissue Simulation Engine Environment.

Project description

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.


Installation

BETSEE is universally installable with either:

  • [Recommended] pip, the standard Python package manager:

    pip3 install betsee
    
  • Anaconda, a third-party Python package manager:

    conda config --add channels conda-forge
    conda install betsee
    

See our installation instructions for details. [1]

[1]Globally replace all instances of the substring betse with betsee (e.g., pip3 install betsee rather than pip3 install betse) in these instructions, which technically refer to BETSE rather than BETSEE.

License

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:

Citation

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). [2] Frontiers in Bioengineering and Biotechnology, 4(55). https://doi.org/10.3389/fbioe.2016.00055

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

[2]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.

Authors

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.

Funding

BETSEE is currently independently financed as a volunteer open-source project. Prior grant funding sources include (in chronological order):

  1. For the three year period spanning 2017—2019, BETSEE was graciously 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 .

Project details


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