Metadata-Version: 2.1
Name: betsee
Version: 0.9.0.0
Summary: BETSEE, the BioElectric Tissue Simulation Engine Environment.
Home-page: https://gitlab.com/betse/betsee
Author: Alexis Pietak, Cecil Curry, et al.
Author-email: leycec@gmail.com
Maintainer: Alexis Pietak, Cecil Curry, et al.
Maintainer-email: leycec@gmail.com
License: 2-clause BSD
Download-URL: https://gitlab.com/betse/betsee/repository/archive.tar.gz?ref=v0.9.0.0
Description: .. # ------------------( BADGES                             )------------------
        .. #FIXME: Depict the current BETSEE rather than BETSE build status after
        .. #creating a BETSEE test suite.
        
        .. image::  https://gitlab.com/betse/betse/badges/master/build.svg
           :target: https://gitlab.com/betse/betse/pipelines
           :alt: Linux Build Status
        .. image::  https://ci.appveyor.com/api/projects/status/mow7y8k3vpfu30c6/branch/master?svg=true
           :target: https://ci.appveyor.com/project/betse/betse/branch/master
           :alt: Windows Build Status
        
        .. # ------------------( SYNOPSIS                           )------------------
        
        ======
        BETSEE
        ======
        
        **BETSEE** (**B**\ io\ **E**\ lectric **T**\ issue **S**\ imulation
        **E**\ ngine **E**\ nvironment) 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 <codebase_>`__ in pure `Python 3
        <Python_>`__, `continuously stress-tested <testing_>`__ with GitLab-CI_ **×**
        Appveyor_ **+** py.test_, and `permissively distributed <License_>`__ 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`_.
        
        .. # ------------------( TABLE OF CONTENTS                  )------------------
        .. # Blank line. By default, Docutils appears to only separate the subsequent
        .. # table of contents heading from the prior paragraph by less than a single
        .. # blank line, hampering this table's readability and aesthetic comeliness.
        
        |
        
        .. # Table of contents, excluding the above document heading. While the
        .. # official reStructuredText documentation suggests that a language-specific
        .. # heading will automatically prepend this table, this does *NOT* appear to
        .. # be the case. Instead, this heading must be explicitly declared.
        
        .. contents:: **Contents**
           :local:
        
        .. # ------------------( DESCRIPTION                        )------------------
        
        Installation
        ============
        
        BETSEE is installable under **Linux**, **macOS**, and **Windows** as follows:
        
        - [\ *Windows*\ ] Emulate **Ubuntu Linux** via the `Windows Subsystem for Linux
          (WSL) <WSL_>`__. [#windows_not]_
        - Install the **Python 3.x** [#python2_not]_ (e.g., 3.6) variant of Anaconda_.
          [#anaconda_not]_
        - Open a **Bash terminal.** [#terminal]_
        - Run the following commands.
        
          - Enable conda-forge_.
        
            .. code-block:: console
        
               conda config --add channels conda-forge
        
          - Install **BETSEE.** [#conda_package]_
        
            .. code-block:: console
        
               conda install betsee
        
          - [\ *Optional*\ ] Run **BETSEE.**
        
            .. code-block:: console
        
               betsee
        
        .. [#windows_not]
           The `Windows Subsystem for Linux (WSL) <WSL_>`__ and – hence BETSEE itself –
           is *only* installable under **Windows 10.** Under older Windows versions,
           BETSEE may be installed from a `virtual Linux guest <VirtualBox_>`__.
        
        .. [#python2_not]
           Do *not* install the **Python 2.7** variant of Anaconda_. BETSEE requires
           **Python 3.x.**
        
        .. [#anaconda_not]
           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 <PyPI 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.
        
        .. [#terminal]
           To open a `POSIX`_\ -compatible terminal under:
        
           - **Windows:**
        
             #. Install **Ubuntu Linux** via the `Windows Subsystem for Linux (WSL) <WSL_>`__.
             #. Open an *Ubuntu Linux terminal.*
        
           - **macOS:**
        
             #. Open the *Finder*.
             #. Open the *Applications* folder.
             #. Open the *Utilities* folder.
             #. Open *Terminal.app*.
        
           - **Ubuntu Linux:**
        
             #. Type ``Ctrl``\ +\ ``Alt``\ +\ ``t``.
        
        .. [#conda_package]
        
           This command installs both the `most recent stable release of BETSEE <conda
           package_>`__ *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
           <conda-forge_>`__.
        
        License
        =======
        
        BETSEE is open-source software `released <LICENSE>`__ under the permissive `BSD
        2-clause license`_. BETSEE contains third-party assets also released under
        `BSD-compatible licenses <license compatibility_>`__, including:
        
        * All `Entypo+ icons`_ `distributed with BETSEE <BETSEE Entypo+ icons_>`__,
          `kindly released <Entypo+ license_>`__ under the permissive `CC BY-SA 4.0
          license`_ by `Daniel Bruce`_.
        * All `Noun Project icons`_ `distributed with BETSEE <BETSEE Noun Project
          icons_>`__, `kindly released <Noun Project license_>`__ under the permissive
          `CC BY 3.0 license`_ by various authors, including:
        
          * `Maxim Kulikov`_, author of the `salubrious bovine <Cows collection_>`__
            prominently displayed on this `project page <project_>`__.
        
        * All `Open Iconic icons`_ `distributed with BETSEE <BETSEE Open Iconic
          icons_>`__, `kindly released <Open Iconic license_>`__ under the permissive
          `MIT license`_.
        
        Citation
        =========
        
        BETSE_ is formally described in our `introductory paper <2016 article_>`__.
        Third-party papers, theses, and other texts leveraging BETSEE (and hence BETSE_)
        should ideally cite the following:
        
            `Alexis Pietak`_ and `Michael Levin`_, 2016. |2016 article name|_
            |2016 article supplement|_ [#supplement]_ |2016 journal name|_ *4*\ (55).
            :sup:`https://doi.org/10.3389/fbioe.2016.00055`
        
        See also `this list of BETSE-centric papers <BETSE citation_>`__ for
        additional material.
        
        .. [#supplement]
           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 <author list_>`__ and
        contributors_ – without whom this project would be computationally impoverished,
        biologically misaligned, and simply unusable.
        
        **Thanks, all.**
        
        .. # ------------------( LINKS ~ betse                      )------------------
        .. _BETSE:
           https://gitlab.com/betse/betse
        .. _BETSE citation:
           https://gitlab.com/betse/betse#citation
        .. _BETSE live:
           https://gitlab.com/betse/betse#advanced
        
        .. # ------------------( LINKS ~ betsee                     )------------------
        .. _author list:
           doc/rst/AUTHORS.rst
        .. _codebase:
           https://gitlab.com/betse/betsee/tree/master
        .. _conda package:
           https://anaconda.org/conda-forge/betsee
        .. _contributors:
           https://gitlab.com/betse/betsee/graphs/master
        .. _dependencies:
           doc/md/INSTALL.md
        .. _project:
           https://gitlab.com/betse/betsee
        .. _PyPI package:
           https://pypi.org/project/betsee
        .. _testing:
           https://gitlab.com/betse/betsee/pipelines
        .. _tarballs:
           https://gitlab.com/betse/betsee/tags
        .. _Ubuntu 16.04 installer:
           https://gitlab.com/betse/betsee/blob/master/bin/install/linux/betsee_ubuntu_16_04.bash
        
        .. # ------------------( LINKS ~ academia                   )------------------
        .. _Alexis Pietak:
        .. _Pietak, Alexis:
           https://www.researchgate.net/profile/Alexis_Pietak
        .. _Michael Levin:
        .. _Levin, Michael:
           https://ase.tufts.edu/biology/labs/levin
        .. _Paul Allen Discovery Center:
           http://www.alleninstitute.org/what-we-do/frontiers-group/discovery-centers/allen-discovery-center-tufts-university
        .. _Paul Allen Discovery Center award:
           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
        .. _Paul G. Allen Frontiers Group:
           https://www.alleninstitute.org/what-we-do/frontiers-group
        .. _Tufts University:
           https://www.tufts.edu
        
        .. # ------------------( LINKS ~ paper : 2016               )------------------
        .. _2016 article:
           http://journal.frontiersin.org/article/10.3389/fbioe.2016.00055/abstract
        
        .. |2016 article name| replace::
           **Exploring instructive physiological signaling with the bioelectric tissue
           simulation engine (BETSE).**
        .. _2016 article name:
           http://journal.frontiersin.org/article/10.3389/fbioe.2016.00055/abstract
        
        .. |2016 article supplement| replace::
           **(**\ Supplement\ **).**
        .. _2016 article supplement:
           https://www.frontiersin.org/articles/file/downloadfile/203679_supplementary-materials_datasheets_1_pdf/octet-stream/Data%20Sheet%201.PDF/1/203679
        
        .. |2016 journal name| replace::
           *Frontiers in Bioengineering and Biotechnology,*
        .. _2016 journal name:
           http://journal.frontiersin.org/journal/bioengineering-and-biotechnology
        
        .. # ------------------( LINKS ~ science                    )------------------
        .. _biochemical reaction networks:
           http://www.nature.com/subjects/biochemical-reaction-networks
        .. _electrodiffusion:
           https://en.wikipedia.org/wiki/Nernst%E2%80%93Planck_equation
        .. _electro-osmosis:
           https://en.wikipedia.org/wiki/Electro-osmosis
        .. _finite volume:
           https://en.wikipedia.org/wiki/Finite_volume_method
        .. _galvanotaxis:
           https://en.wiktionary.org/wiki/galvanotaxis
        .. _gene regulatory networks:
           https://en.wikipedia.org/wiki/Gene_regulatory_network
        .. _voltage-gated ion channels:
           https://en.wikipedia.org/wiki/Voltage-gated_ion_channel
        
        .. # ------------------( LINKS ~ os : linux                 )------------------
        .. _APT:
           https://en.wikipedia.org/wiki/Advanced_Packaging_Tool
        .. _Arch Linux:
           https://www.archlinux.org
        .. _CentOS:
           https://www.centos.org
        .. _Gentoo Linux:
           https://gentoo.org
        .. _Ubuntu:
        .. _Ubuntu Linux:
           https://www.ubuntu.com
        .. _Ubuntu Linux 16.04 (Xenial Xerus):
           http://releases.ubuntu.com/16.04
        
        .. # ------------------( LINKS ~ os : windows               )------------------
        .. _WSL:
           https://msdn.microsoft.com/en-us/commandline/wsl/install-win10
        
        .. # ------------------( LINKS ~ software                   )------------------
        .. _Appveyor:
           https://ci.appveyor.com/project/betse/betse/branch/master
        .. _Bash on Ubuntu on Windows:
           http://www.windowscentral.com/how-install-bash-shell-command-line-windows-10
        .. _FFmpeg:
           https://ffmpeg.org
        .. _Git:
           https://git-scm.com/downloads
        .. _GitLab-CI:
           https://about.gitlab.com/gitlab-ci
        .. _Graphviz:
           http://www.graphviz.org
        .. _Homebrew:
           http://brew.sh
        .. _Libav:
           https://libav.org
        .. _macOS:
           https://en.wikipedia.org/wiki/Macintosh_operating_systems
        .. _MacPorts:
           https://www.macports.org
        .. _Matplotlib:
           http://matplotlib.org
        .. _Miniconda:
           https://conda.io/miniconda.html
        .. _NumPy:
           http://www.numpy.org
        .. _MEncoder:
           https://en.wikipedia.org/wiki/MEncoder
        .. _OpenBLAS:
           https://www.openblas.net
        .. _POSIX:
           https://en.wikipedia.org/wiki/POSIX
        .. _PPA:
           https://launchpad.net/ubuntu/+ppas
        .. _PyPI:
           https://pypi.python.org
        .. _Python:
           https://www.python.org
        .. _py.test:
           http://pytest.org
        .. _SciPy:
           http://www.scipy.org
        .. _VirtualBox:
           https://www.virtualbox.org
        .. _YAML:
           http://yaml.org
        
        .. # ------------------( LINKS ~ software : conda           )------------------
        .. _Anaconda:
           https://www.anaconda.com/download
        .. _Anaconda packages:
           https://anaconda.org
        .. _conda-forge:
           https://conda-forge.org
        
        .. # ------------------( LINKS ~ software : icon            )------------------
        .. _BETSEE Entypo+ icons:
           betsee/data/qrc/icon/entypo+
        .. _BETSEE Noun Project icons:
           betsee/data/qrc/icon/nounproject
        .. _BETSEE Open Iconic icons:
           betsee/data/qrc/icon/open_iconic
        .. _Cows collection:
           https://thenounproject.com/maxim221/collection/cows
        .. _Daniel Bruce:
           http://www.danielbruce.se
        .. _Entypo+ icons:
           http://entypo.com
        .. _Maxim Kulikov:
           https://thenounproject.com/maxim221
        .. _Noun Project:
        .. _Noun Project icons:
           https://thenounproject.com
        .. _Noun Project license:
           https://thenounproject.com/legal
        .. _Open Iconic icons:
           https://github.com/iconic/open-iconic
        
        .. # ------------------( LINKS ~ software : pyside2         )------------------
        .. _PySide2:
           https://wiki.qt.io/PySide2
        .. _PySide2 5.9:
           http://code.qt.io/cgit/pyside/pyside-setup.git/log/?h=5.9
        .. _PySide2 feedstock:
           https://github.com/conda-forge/pyside2-feedstock
        .. _PySide2 installation:
           https://wiki.qt.io/PySide2_GettingStarted
        .. _PySide2 PPA:
           https://launchpad.net/~thopiekar/+archive/ubuntu/pyside-git
        .. _PySide2 wheels:
           https://github.com/fredrikaverpil/pyside2-wheels/blob/master/QUICKSTART.md
        .. _Qt:
           https://www.qt.io
        .. _Qt 5.9:
           https://wiki.qt.io/Qt_5.9_Release
        
        .. # ------------------( LINKS ~ software : licenses        )------------------
        .. _license compatibility:
           https://en.wikipedia.org/wiki/License_compatibility#Compatibility_of_FOSS_licenses
        .. _BSD 2-clause license:
           https://opensource.org/licenses/BSD-2-Clause
        .. _CC BY 3.0 license:
           https://creativecommons.org/licenses/by/3.0
        .. _CC BY-SA 4.0 license:
           https://creativecommons.org/licenses/by-sa/4.0
        .. _Entypo+ license:
           licenses/entypo+
        .. _MIT license:
           https://opensource.org/licenses/MIT
        .. _Open Iconic license:
           licenses/open_iconic
        
Keywords: biology,multiphysics,science,simulator
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: MacOS X
Classifier: Environment :: Win32 (MS Windows)
Classifier: Environment :: X11 Applications
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Provides-Extra: all
