betsee 0.8.1.0

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

Note

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:

• Platform-agnostic BETSEE packages (e.g., Anaconda, PyPI).

• Platform-specific BETSEE packages (e.g., macOS Homebrew, Ubuntu PPA).

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 https://gitlab.com/betse/betsee/raw/master/bin/install/linux/betsee_ubuntu_16_04.bash && 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 https://gitlab.com/betse/betsee.git

   6. Install BETSEE.

      cd betsee
      sudo python3 setup.py 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 Terminal.app.

• 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:

• Arch Linux via the official PySide2 installation instructions.

• Gentoo Linux via the official PySide2 installation instructions.

• Most other platforms (e.g., Ubuntu Linux, CentOS, macOS, Windows) via the unofficial PySide2 wheels.

• The platform-agnostic Anaconda and Miniconda Python distributions via the unofficial PySide2 conda-forge feedstock.

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

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.

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.