betsee 0.9.0.0

BETSEE, the BioElectric Tissue Simulation Engine Environment.

BETSEE

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

• Installation

• License

• Citation

• Authors

Installation

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:

• 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 Terminal.app.

• 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.

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). [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.

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.