BETSEE, the BioElectric Tissue Simulation Engine Environment.
pip install betsee==0.8.2.0
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.
Contents
BETSEE is installable under Linux, macOS, and Windows as follows:
[Windows] Emulate Ubuntu Linux via the Windows Subsystem for Linux (WSL). [1]
Install the Python 3.x [2] (e.g., 3.6) variant of Anaconda. [3]
Open a Bash terminal. [4]
Run the following commands.
Enable conda-forge.
conda config --add channels conda-forge
Install BETSEE. [5]
conda install betsee
[Optional] Run BETSEE.
betsee
[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. |
[4] |
To open a POSIX-compatible terminal under:
|
[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). https://doi.org/10.3389/fbioe.2016.00055
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.