{ "info": { "author": "Alexis Pietak, Cecil Curry, et al.", "author_email": "leycec@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Environment :: MacOS X", "Environment :: Win32 (MS Windows)", "Environment :: X11 Applications", "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Natural Language :: English", "Operating System :: OS Independent", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": ".. # ------------------( DIRECTIVES )------------------\n.. # Fallback language applied to all code blocks failing to specify an\n.. # explicit language. Since the majority of all code blocks in this document\n.. # are Bash one-liners intended to be run interactively, this is \"console\".\n.. # For a list of all supported languages, see also:\n.. # http://build-me-the-docs-please.readthedocs.org/en/latest/Using_Sphinx/ShowingCodeExamplesInSphinx.html#pygments-lexers\n\n.. # FIXME: Sadly, this appears to be unsupported by some ReST parsers and hence\n.. # is disabled until more widely supported. *collective shrug*\n.. # highlight:: console\n\n.. # ------------------( SYNOPSIS )------------------\n\n======\nBETSEE\n======\n\n**BETSEE** (**B**\\ io\\ **E**\\ lectric **T**\\ issue **S**\\ imulation **E**\\\nngine **E**\\ nvironment) is the open-source cross-platform graphical user\ninterface (GUI) for BETSE_, a `finite volume`_ simulator for 2D computational\nmultiphysics problems in the life sciences \u2013 including electrodiffusion_,\nelectro-osmosis_, galvanotaxis_, `voltage-gated ion channels`_, `gene\nregulatory networks`_, and `biochemical reaction networks`_ (e.g., metabolism).\n\nLike BETSE_, BETSEE is `portably implemented `__ in pure `Python 3\n`__, `continuously stress-tested `__ with GitLab-CI_ **\u00d7**\nAppveyor_ **+** py.test_, and `permissively distributed `__ under the\n`BSD 2-clause license`_.\n\n.. # ------------------( TABLE OF CONTENTS )------------------\n.. # Blank line. By default, Docutils appears to only separate the subsequent\n.. # table of contents heading from the prior paragraph by less than a single\n.. # blank line, hampering this table's readability and aesthetic comeliness.\n\n|\n\n.. # Table of contents, excluding the above document heading. While the\n.. # official reStructuredText documentation suggests that a language-specific\n.. # heading will automatically prepend this table, this does *NOT* appear to\n.. # be the case. Instead, this heading must be explicitly declared.\n\n.. contents:: **Contents**\n :local:\n\n.. # ------------------( DESCRIPTION )------------------\n\nInstallation\n============\n\nBETSEE is installable under **Linux**, **macOS**, and **Windows** as follows:\n\n- [\\ *Windows*\\ ] Emulate **Ubuntu Linux** via the `Windows Subsystem for Linux\n (WSL) `__. [#windows_not]_\n- Install the **Python 3.x** [#python2_not]_ (e.g., 3.6) variant of Anaconda_.\n [#anaconda_not]_\n- Open a **Bash terminal.** [#terminal]_\n- Run the following commands.\n\n - Enable conda-forge_.\n\n .. code-block:: console\n\n conda config --add channels conda-forge\n\n - Install **BETSEE.** [#conda_package]_\n\n .. code-block:: console\n\n conda install betsee\n\n - [\\ *Optional*\\ ] Run **BETSEE.**\n\n .. code-block:: console\n\n betsee\n\n.. [#windows_not]\n The `Windows Subsystem for Linux (WSL) `__ and \u2013 hence BETSEE itself \u2013\n is *only* installable under **Windows 10.** Under older Windows versions,\n BETSEE may be installed from a `virtual Linux guest `__.\n\n.. [#python2_not]\n Do *not* install the **Python 2.7** variant of Anaconda_. BETSEE requires\n **Python 3.x.**\n\n.. [#anaconda_not]\n BETSEE is currently *only* installable via Anaconda_, a cross-platform\n scientific Python distribution simplifying installation of non-Python\n dependencies (e.g., OpenBLAS_, PySide2_). While a `PyPI package`_ for\n installing BETSEE under ``pip`` (the standard Python package manager) does\n exist, `that package `__ is currently uninstallable due to\n a lack of official PySide2_ wheels. Even when official PySide2_ wheels are\n published, Anaconda_ will remain the official installation path for BETSE_\n and hence BETSEE. ``pip`` commonly produces a performance-crippled\n single-core installation of BETSE_. Anaconda_ suffers no such issues and is\n guaranteed to produce a performance-optimized multicore installation of\n BETSE_ on *all* supported platforms. We strongly recommend Anaconda_ \u2013 even\n when you think you know better.\n\n.. [#terminal]\n To open a `POSIX`_\\ -compatible terminal under:\n\n - **Windows:**\n\n #. Install **Ubuntu Linux** via the `Windows Subsystem for Linux (WSL) `__.\n #. Open an *Ubuntu Linux terminal.*\n\n - **macOS:**\n\n #. Open the *Finder*.\n #. Open the *Applications* folder.\n #. Open the *Utilities* folder.\n #. Open *Terminal.app*.\n\n - **Ubuntu Linux:**\n\n #. Type ``Ctrl``\\ +\\ ``Alt``\\ +\\ ``t``.\n\n.. [#conda_package]\n\n This command installs both the `most recent stable release of BETSEE `__ *and* all mandatory and most optional dependencies of this\n release. Older stable releases are installable in a similar manner (e.g.,\n ``conda install betsee=0.8.2`` for BETSEE 0.8.2). All `Anaconda packages`_\n are kindly hosted by the `non-profit conda-forge organization\n `__.\n\nLicense\n=======\n\nBETSEE is open-source software `released `__ under the permissive `BSD\n2-clause license`_. BETSEE contains third-party assets also released under\n`BSD-compatible licenses `__, including:\n\n* All `Entypo+ icons`_ `distributed with BETSEE `__,\n `kindly released `__ under the permissive `CC BY-SA 4.0\n license`_ by `Daniel Bruce`_.\n* All `Noun Project icons`_ `distributed with BETSEE `__, `kindly released `__ under the permissive\n `CC BY 3.0 license`_ by various authors, including:\n\n * `Maxim Kulikov`_, author of the `salubrious bovine `__\n prominently displayed on this `project page `__.\n\n* All `Open Iconic icons`_ `distributed with BETSEE `__, `kindly released `__ under the permissive\n `MIT license`_.\n\nCitation\n=========\n\nBETSE_ is formally described in our `introductory paper <2016 article_>`__.\nThird-party papers, theses, and other texts leveraging BETSEE (and hence\nBETSE_) should ideally cite the following:\n\n `Alexis Pietak`_ and `Michael Levin`_, 2016. |2016 article name|_\n |2016 article supplement|_ [#supplement]_ |2016 journal name|_ *4*\\ (55).\n :sup:`https://doi.org/10.3389/fbioe.2016.00055`\n\nSee also `this list of BETSE-centric papers `__ for\nadditional material.\n\n.. [#supplement]\n This article's supplement extends the cursory theory presented by this\n article with a rigorous treatment of the mathematics, formalisms, and\n abstractions required to fully reproduce this work. If theoretical questions\n remain after completing the main article, please consult this supplement.\n\nAuthors\n=======\n\nBETSEE comes courtesy a dedicated community of `authors `__ and\ncontributors_ \u2013 without whom this project would be computationally\nimpoverished, biologically misaligned, and simply unusable.\n\n**Thanks, all.**\n\nFunding\n=======\n\nBETSEE is currently independently financed as a volunteer open-source project.\nPrior grant funding sources include (in chronological order):\n\n#. For the three year period spanning 2017\u20142019, BETSEE was graciously\n associated with the `Paul Allen Discovery Center`_ at `Tufts University`_\n and supported by a `Paul Allen Discovery Center award`_ from the `Paul G.\n Allen Frontiers Group`_ .\n\n.. # ------------------( LINKS ~ betse )------------------\n.. _BETSE:\n https://gitlab.com/betse/betse\n.. _BETSE citation:\n https://gitlab.com/betse/betse#citation\n.. _BETSE live:\n https://gitlab.com/betse/betse#advanced\n\n.. # ------------------( LINKS ~ betsee )------------------\n.. _author list:\n doc/rst/AUTHORS.rst\n.. _codebase:\n https://gitlab.com/betse/betsee/tree/master\n.. _conda package:\n https://anaconda.org/conda-forge/betsee\n.. _contributors:\n https://gitlab.com/betse/betsee/graphs/master\n.. _dependencies:\n doc/md/INSTALL.md\n.. _project:\n https://gitlab.com/betse/betsee\n.. _PyPI package:\n https://pypi.org/project/betsee\n.. _testing:\n https://gitlab.com/betse/betsee/pipelines\n.. _tarballs:\n https://gitlab.com/betse/betsee/tags\n.. _Ubuntu 16.04 installer:\n https://gitlab.com/betse/betsee/blob/master/bin/install/linux/betsee_ubuntu_16_04.bash\n\n.. # ------------------( LINKS ~ academia )------------------\n.. _Alexis Pietak:\n.. _Pietak, Alexis:\n https://www.researchgate.net/profile/Alexis_Pietak\n.. _Michael Levin:\n.. _Levin, Michael:\n https://ase.tufts.edu/biology/labs/levin\n.. _Paul Allen Discovery Center:\n http://www.alleninstitute.org/what-we-do/frontiers-group/discovery-centers/allen-discovery-center-tufts-university\n.. _Paul Allen Discovery Center award:\n https://www.alleninstitute.org/what-we-do/frontiers-group/news-press/press-resources/press-releases/paul-g-allen-frontiers-group-announces-allen-discovery-center-tufts-university\n.. _Paul G. Allen Frontiers Group:\n https://www.alleninstitute.org/what-we-do/frontiers-group\n.. _Tufts University:\n https://www.tufts.edu\n\n.. # ------------------( LINKS ~ paper : 2016 )------------------\n.. _2016 article:\n http://journal.frontiersin.org/article/10.3389/fbioe.2016.00055/abstract\n\n.. |2016 article name| replace::\n **Exploring instructive physiological signaling with the bioelectric tissue\n simulation engine (BETSE).**\n.. _2016 article name:\n http://journal.frontiersin.org/article/10.3389/fbioe.2016.00055/abstract\n\n.. |2016 article supplement| replace::\n **(**\\ Supplement\\ **).**\n.. _2016 article supplement:\n https://www.frontiersin.org/articles/file/downloadfile/203679_supplementary-materials_datasheets_1_pdf/octet-stream/Data%20Sheet%201.PDF/1/203679\n\n.. |2016 journal name| replace::\n *Frontiers in Bioengineering and Biotechnology,*\n.. _2016 journal name:\n http://journal.frontiersin.org/journal/bioengineering-and-biotechnology\n\n.. # ------------------( LINKS ~ science )------------------\n.. _biochemical reaction networks:\n http://www.nature.com/subjects/biochemical-reaction-networks\n.. _electrodiffusion:\n https://en.wikipedia.org/wiki/Nernst%E2%80%93Planck_equation\n.. _electro-osmosis:\n https://en.wikipedia.org/wiki/Electro-osmosis\n.. _finite volume:\n https://en.wikipedia.org/wiki/Finite_volume_method\n.. _galvanotaxis:\n https://en.wiktionary.org/wiki/galvanotaxis\n.. _gene regulatory networks:\n https://en.wikipedia.org/wiki/Gene_regulatory_network\n.. _voltage-gated ion channels:\n https://en.wikipedia.org/wiki/Voltage-gated_ion_channel\n\n.. # ------------------( LINKS ~ os : linux )------------------\n.. _APT:\n https://en.wikipedia.org/wiki/Advanced_Packaging_Tool\n.. _Arch Linux:\n https://www.archlinux.org\n.. _CentOS:\n https://www.centos.org\n.. _Gentoo Linux:\n https://gentoo.org\n.. _Ubuntu:\n.. _Ubuntu Linux:\n https://www.ubuntu.com\n.. _Ubuntu Linux 16.04 (Xenial Xerus):\n http://releases.ubuntu.com/16.04\n\n.. 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https://thenounproject.com/maxim221\n.. _Noun Project:\n.. _Noun Project icons:\n https://thenounproject.com\n.. _Noun Project license:\n https://thenounproject.com/legal\n.. _Open Iconic icons:\n https://github.com/iconic/open-iconic\n\n.. # ------------------( LINKS ~ software : pyside2 )------------------\n.. _PySide2:\n https://wiki.qt.io/PySide2\n.. _PySide2 5.9:\n http://code.qt.io/cgit/pyside/pyside-setup.git/log/?h=5.9\n.. _PySide2 feedstock:\n https://github.com/conda-forge/pyside2-feedstock\n.. _PySide2 installation:\n https://wiki.qt.io/PySide2_GettingStarted\n.. _PySide2 PPA:\n https://launchpad.net/~thopiekar/+archive/ubuntu/pyside-git\n.. _PySide2 wheels:\n https://github.com/fredrikaverpil/pyside2-wheels/blob/master/QUICKSTART.md\n.. _Qt:\n https://www.qt.io\n.. _Qt 5.9:\n https://wiki.qt.io/Qt_5.9_Release\n\n.. # ------------------( LINKS ~ software : licenses )------------------\n.. _license compatibility:\n 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