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]
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:
All Entypo+ icons distributed with BETSEE, kindly released under the permissive CC BY-SA 4.0 license by Daniel Bruce.
All Noun Project icons distributed with BETSEE, kindly released under the permissive CC BY 3.0 license by various authors, including:
Maxim Kulikov, author of the salubrious bovine prominently displayed on this project page.
All Open Iconic icons distributed with BETSEE, kindly released under the permissive MIT license.
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.
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.
Funding
BETSEE is currently independently financed as a volunteer open-source project. Prior grant funding sources include (in chronological order):
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 .
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