Metadata-Version: 2.1
Name: betse
Version: 0.9.2
Summary: BETSE, the BioElectric Tissue Simulation Engine.
Home-page: https://gitlab.com/betse/betse
Author: Alexis Pietak, Cecil Curry, et al.
Author-email: alexis.pietak@gmail.com
Maintainer: Alexis Pietak, Cecil Curry, et al.
Maintainer-email: alexis.pietak@gmail.com
License: 2-clause BSD
Download-URL: https://gitlab.com/betse/betse/repository/archive.tar.gz?ref=v0.9.2
Description: .. # ------------------( DIRECTIVES                         )------------------
        .. # Fallback language applied to all code blocks failing to specify an
        .. # explicit language. Since the majority of all code blocks in this document
        .. # are Bash one-liners intended to be run interactively, this is "console".
        .. # For a list of all supported languages, see also:
        .. #     http://build-me-the-docs-please.readthedocs.org/en/latest/Using_Sphinx/ShowingCodeExamplesInSphinx.html#pygments-lexers
        
        .. # FIXME: Sadly, this appears to be unsupported by some ReST parsers and hence
        .. # is disabled until more widely supported. *collective shrug*
        .. # highlight:: console
        
        .. # ------------------( SYNOPSIS                           )------------------
        
        =====
        BETSE
        =====
        
        **BETSE** (**B**\ io\ **E**\ lectric **T**\ issue **S**\ imulation **E**\
        ngine) is an open-source cross-platform `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). BETSE is 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`_.
        
        BETSE is `portably implemented <codebase_>`__ in pure `Python 3`_,
        `continuously stress-tested <testing_>`__ with GitLab-CI_ **×** Appveyor_ **+**
        py.test_, and `permissively distributed <License_>`__ under the `BSD 2-clause
        license`_.
        
        ======
        BETSEE
        ======
        
        BETSEE_ (\ **BETSE E**\ nvironment) is the official open-source cross-platform
        graphical user interface (GUI) for BETSE. BETSEE_ wraps the low-level
        command-line interface (CLI) bundled with BETSE in a high-level interactive
        modelling environment optimized for both new and advanced users alike.
        
        Like BETSE, BETSEE_ is `portably implemented <BETSEE codebase_>`__ in `Python
        3`_ and `permissively distributed <License_>`__ under the `BSD 2-clause
        license`_. Unlike BETSE, BETSEE_ leverages the industry-standard PySide2_-based
        `Qt 5 <Qt_>`_ application framework to deliver a modern scientific workflow.
        
        .. # ------------------( 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
        ============
        
        BETSE currently supports **Linux**, **macOS**, and **Windows** out-of-the-box.
        
        Simple
        --------
        
        For new users, BETSE is portably installable 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 **BETSE.** [#conda_package]_
          
            .. code-block:: console
        
               conda install betse
          
          - [\ *Optional*\ ] Test **BETSE.** [#test_command]_
        
            .. code-block:: console
        
               betse -v try
        
        .. [#windows_not]
           The `Windows Subsystem for Linux (WSL) <WSL_>`__ and – hence BETSE itself –
           is *only* installable under **Windows 10.** Under older Windows versions,
           BETSE may be installed from a `virtual Linux guest <VirtualBox_>`__.
        
        .. [#python2_not]
           Do *not* install the **Python 2.7** variant of Anaconda_. BETSE requires
           **Python 3.x.**
        
        .. [#anaconda_not]
           If you prefer *not* to install Anaconda_, BETSE dependencies are also
           `manually installable <Advanced_>`__ via your platform-specific package
           manager (e.g., Homebrew_ on macOS, APT_ on Ubuntu Linux). Doing so is
           non-trivial and, where performed incorrectly, could produce 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 BETSE <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 betse=0.7.0`` for BETSE 0.7.0). All `Anaconda packages`_ are
           kindly hosted by the `non-profit conda-forge organization <conda-forge_>`__.
        
        .. [#test_command]
        
           This test command:
        
           #. Enables verbosity with the ``-v`` option, simplifying issue reporting in
              the event of an unexpected error.
           #. Creates a ``sample_sim/`` subdirectory in the current directory, providing
              the default simulation for this release of BETSE. This includes *all*
              configuration files and resources referenced by these files.
           #. Runs all simulation phases (e.g., seed, initialization) of this simulation.
        
           When finished, you may safely either:
           
           - Remove this subdirectory.
           - Rename this subdirectory (e.g., to ``my_sim/``) to serve as a basis for
             subsequent simulations.
           - Preserve this subdirectory as is.
        
        Advanced
        --------
        
        For developers and advanced users, *any* version of BETSE – including the live
        repository and prior stable releases – is manually installable as follows:
        
        #. Install **Python 3.x** and `all dependencies <dependencies_>`__ required by
           BETSE. Under:
        
           - **Linux,** install `these dependencies <dependencies_>`__ via your
             distribution-specific package manager (e.g., APT_ under Debian-based
             distributions). Do *not* use ``pip``.\ [#pip_not]_
           - **macOS,** either:
        
             - (\ *Recommended*\ ) Install the **Python 3.x** variant of Anaconda_.
             - Or both:
        
               #. Install a third-party package manager (e.g., Homebrew_, MacPorts_).
                  Apple does *not* provide a package manager out-of-the-box.
               #. Install `these dependencies <dependencies_>`__ via that package
                  manager. Do *not* use ``pip``.\ [#pip_not]_
        
           - **Windows,** install the **Python 3.x** variant of Anaconda_.\ [#windows]_
        
        #. Open a **terminal.**
        #. **Download** either:
        
           - **The unstable BETSE repository** as follows:
        
             #. Install Git_.
             #. Clone the ``master`` branch of this repository.
        
                .. code-block:: console
        
                   git clone https://gitlab.com/betse/betse.git
        
             #. Prepare for installation.
        
                .. code-block:: console
        
                   cd betse
        
           - **Any stable BETSE release,** including the most recent, as follows:
        
             #. Visit our `source tarball archive <tarballs_>`__.
             #. Click the download icon to the right of the desired release and select
                *Download tar.gz*.
             #. Extract the downloaded tarball into the current directory.
        
                .. code-block:: console
        
                   tar -xvzf betse-*.tar.gz
        
             #. (\ *Optional*\ ) Remove this tarball.
        
                .. code-block:: console
        
                   rm betse-*.tar.gz
        
             #. Prepare for installation.
        
                .. code-block:: console
        
                   cd betse-*
        
        #. **Install BETSE** either:
        
           - (\ *Recommended*\ ) **Editably,** installing a cross-platform symbolic link
             to the current BETSE codebase. Modifications to this code are applied
             immediately *without* requiring reinstallation.
        
             .. code-block:: console
        
                sudo python3 setup.py develop
        
           - **Non-editably,** installing a physical copy of the current BETSE codebase.
             Modifications to this code are ignored and thus require reinstallation.
        
             .. code-block:: console
        
                sudo python3 setup.py install
        
        #. (\ *Optional*\ ) **Test BETSE,** running all modelling phases of a sample
           simulation from a new directory.
        
           .. code-block:: console
        
              cd /tmp && betse try
        
        
        .. [#pip_not]
           Do *not* install scientific dependencies (e.g., NumPy_, SciPy_) with either
           ``pip`` or ``easy_install``; doing so typically degrades BETSE to single-core
           performance. To optimize BETSE across multiple cores, *always* install these
           dependencies with your platform-specific package manager (e.g., Homebrew_,
           APT_).
        
        .. [#windows]
           Unlike Linux and macOS, Anaconda_ is (\ *effectively*\ ) required under
           Windows. Due to Microsoft's lack of support for `POSIX`_\ -compliant
           toolchains, *no* reasonable alternatives for installing multicore-aware
           scientific dependencies exist.
        
        Usage
        ============
        
        Basic
        -----
        
        BETSE installs the ``betse`` command, a low-level command line interface (CLI)
        designed for experienced users. The typical CLI-based workflow resembles:
        
        #. Create a default simulation configuration in a new ``my_sim/`` subdirectory
           of the current directory.
        
           .. code-block:: console
        
              betse config my_sim/sim_config.yml
        
        #. [\ *Optional*\ ] Edit the new ``my_sim/sim_config.yml`` file with `your
           favourite text editor <Atom_>`__.
        #. Create a pseudo-random cell cluster from this simulation configuration.
        
           .. code-block:: console
        
              betse seed my_sim/sim_config.yml
        
        #. [\ *Optional*\ ] Export all enabled plots, animations, and comma-separated
           value (CSV) files from this cell cluster.
        
           .. code-block:: console
        
              betse plot seed my_sim/sim_config.yml
        
        #. Initialize (i.e., calculate steady-state concentrations for) this cell cluster.
        
           .. code-block:: console
        
              betse init my_sim/sim_config.yml
        
        #. [\ *Optional*\ ] Export all enabled plots, animations, and comma-separated
           value (CSV) files from this initialization.
        
           .. code-block:: console
        
              betse plot init my_sim/sim_config.yml
        
        #. Simulate this initialized cell cluster.
        
           .. code-block:: console
        
              betse sim my_sim/sim_config.yml
        
        #. [\ *Optional*\ ] Export all enabled plots, animations, and comma-separated
           value (CSV) files from this simulation.
        
           .. code-block:: console
        
              betse plot sim my_sim/sim_config.yml
        
        Also note that our sister project BETSEE_ installs the ``betsee`` command, a
        high-level graphical user interface (GUI) designed for *all* users – regardless
        of prior experience or familiarity with the command line.
        
        Expert
        --------
        
        BETSE provides a variety of command-line options and subcommands in addition to
        those synopsized above. The standalone ``betse`` and ``betse --help`` commands
        describe these options and subcommands as follows:
        
        .. code-block:: console
        
           usage: betse [-h] [-v] [-V] [--log-file LOG_FILENAME]
                        [--log-level {all,debug,info,warning,error,critical,none}]
                        [--profile-type {none,call,size}]
                        [--profile-file PROFILE_FILENAME]
                        [--matplotlib-backend MATPLOTLIB_BACKEND_NAME]
                        {config,seed,init,sim,sim-grn,plot,info,try} ...
           
           The BioElectric Tissue Simulation Engine (BETSE) is 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.
           
           optional arguments:
             -h, --help            show this help message and exit
             -v, --verbose         print and log all messages verbosely
             -V, --version         print program version and exit
             --log-file LOG_FILENAME
                                   file to log to (defaults to
                                   "/home/leycec/.betse/betse.log")
             --log-level {all,debug,info,warning,error,critical,none}
                                   minimum level of messages to log to "--log-file"
                                   (defaults to "info") [overridden by "--verbose"]
             --profile-type {none,call,size}
                                   type of profiling to perform (defaults to "none"):
                                   * "none", disabling profiling
                                   * "call", profiling callables (functions, methods)
                                   * "size", profiling object sizes (requires "pympler")
             --profile-file PROFILE_FILENAME
                                   file to profile to unless "--profile-type=none"
                                   (defaults to "/home/leycec/.betse/betse.prof")
             --matplotlib-backend MATPLOTLIB_BACKEND_NAME
                                   name of matplotlib backend to use (see: "betse info")
           
           subcommands:
           Exactly one of the following subcommands must be passed:
           
             {config,seed,init,sim,sim-grn,plot,info,try}
               config              create a default config file for BETSE simulations
               seed                seed a new cell cluster for a config file
               init                initialize a seeded cell cluster for a config file
               sim                 simulate an initialized cell cluster for a config file
               sim-grn             simulate a gene regulatory network for a config file
               plot                plot an initialized or simulated simulation
               info                print metadata synopsizing BETSE and current system
               try                 create, init, simulate, and plot a sample simulation
           
           subcommand help:
           
           For help with a specific subcommand, pass the "-h" or "--help" option to that
           subcommand. For example, for help with the "config" subcommand, run:
           
               betse config --help
        
        Documentation
        -------------
        
        BETSE also provides external documentation optimized for offline reading –
        complete with explanatory examples, sample plots, and ample screenshots:
        
        - Official `BETSE 0.4 documentation`_. (\ *PDF format; 72 pages.*\ )
        - Official `BETSE 0.3 documentation`_. (\ *PDF format; 77 pages.*\ )
        
        Introduction
        ============
        
        BETSE simulates biorealistic electrochemical phenomena in `gap junction`_\
        -networked 2D cellular collectives. To predict `bioelectric patterns
        <bioelectricity_>`__ and their spatio-temporal dynamics, BETSE:
        
        - Models `ion channel`_ and `gap junction`_ activity.
        - Tracks changes in ion concentration and net ionic charge.
        - Calculates endogenous voltages and currents.
        - Accepts simulation parameters, variables, and options as human-readable,
          well-commented configuration files in YAML_ format.
        - Exports simulation results to a variety of output formats, including:
        
          - Publication-quality:
        
            - Plots, charts, and animations driven by Matplotlib_, the industry
              standard for open-source plot visualization.
            - `Directed graphs`_ (i.e., networks) driven by Graphviz_, the industry
              standard for open-source graph visualization.
        
          - Internet-friendly compressed video driven by any of various popular
            open-source video encoders, including FFmpeg_, Libav_, and MEncoder_.
          - Post-processable tabular data (e.g., `comma-separated values (CSV)
            <comma-separated values_>`__).
        
        - Imports bitmask images defining the shapes of:
        
          - Cell clusters.
          - Cell cluster regions localizing `ion channel`_ activity, typically
            signifying disparate types of adjacent tissue.
        
        To assemble simple concepts into complex simulations, BETSE supplies a richly
        configurable, highly scalable biological toolset consisting of:
        
        Ions
        ----
        
        Simulations may enable arbitrary combinations of the principal ions implicated
        in bioelectrical signaling – including:
        
        - Sodium_ (*Na*\ :sup:`+`).
        - Potassium_ (*K*\ :sup:`+`).
        - Chloride_ (*Cl*\ :sup:`-`).
        - Calcium_ (*Ca*\ :sup:`2+`).
        - Hydrogen_ (*H*\ :sup:`+`).
        - `Anionic proteins`_ (*P*\ :sup:`-`).
        - Bicarbonate_ (*HCO*\ :sup:`-`\ :sub:`3`).
        
        Ion Channels
        ------------
        
        Individual cells in simulations may enable arbitrary combinations of
        `voltage-gated ion channels`_, each implementing the `Hodgkin-Huxley (HH)
        formalism`_ with experimentally-derived parameters sourced from reputable
        `knowledge-based systems`_ (e.g., Channelpedia_). Explicitly supported channel
        types include:
        
        - HCN1_, HCN2_, and HCN4_.
        - `L-type Ca`_, `T-type Ca`_, and |P/Q-type Ca|_.
        - Kir2.1_.
        - Kv1.1_, Kv1.2_, Kv1.5_. Kv3.3_, and Kv3.4_.
        - Nav1.2_, Nav1.3_, and Nav1.6_.
        - `Leak <leak channels_>`__ and `ligand-gated channels`_, including:
        
          - |Calcium-gated K+ channels|_.
        
        Custom ion channels parametrized by user-selected constants may be trivially
        defined in the same manner (e.g., via a YAML_\ -formatted configuration file).
        
        Ion Pumps and Exchangers
        ------------------------
        
        For fine-grained control over cell dynamics, notable ion pumps and exchangers
        may also be selectively enabled – including:
        
        - |Ca2+-ATPase|_.
        - |H+/K+-ATPase|_.
        - |Na+/K+-ATPase|_.
        - V-ATPase_.
        
        Custom ion pumps and exchangers parametrized by user-selected constants may be
        trivially defined in the same manner (e.g., via a YAML_\ -formatted
        configuration file).
        
        Extracellular Space
        -------------------
        
        Cells form interconnected intracellular networks via voltage-sensitive `gap
        junction connections <gap junction_>`__ embedded within an `extracellular
        environment`_, maintained by `tight junctions`_ at the cell cluster periphery.
        Simulation of this environment enables exploration of `local field
        potentials`_, `transepithelial potential`_, and `ephaptic coupling`_ between
        cells.
        
        Biological Networks
        -------------------
        
        Simulation of `gene regulatory <gene regulatory networks_>`__ and `biochemical
        reaction networks`_ at both the cellular and mitochondrial level supports deep
        spatial analysis of otherwise intractable biological processes. Metabolism,
        disease, aging, and other `genetic <genetics_>`__ and `epigenetic
        <epigenetics_>`__ phenomena commonly associated with quasi-`Big Data`_ are all
        valid targets for exhaustive study with BETSE.
        
        To integrate these potent control systems with bioelectrical signaling, the
        `activity <enzyme activity_>`__-modulated interaction between `gene products`_
        and similar biochemicals is fully integrated with `ion channels <ion
        channel_>`__, `ion pumps`_, and `gap junctions`_.
        
        Validation
        ==========
        
        BETSE is peer-reviewed software receiving continual evidence-based scrutiny.
        Simulation output is reproducibly synchronized with experimental observations on
        `membrane permeability`_, `resting potential`_, ion concentration, and similar
        real-world biophysical quantities. Predictable outcomes have been demonstrated
        for such well-known cases as:
        
        -  `Transmembrane voltage changes <transmembrane voltage_>`__ on perturbations
           to single cell membrane states and environmental ion concentrations.
        -  `Transepithelial potential differences (TEPD) <transepithelial
           potential_>`__.
        -  Bioelectrical signals at large-scale cellular wound sites.
        
        Citation
        ========
        
        BETSE is formally described in our `introductory paper <2016 article_>`__.
        Third-party papers, theses, and other texts leveraging 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`
        
        Subsequent papers expanding the BETSE architecture with additional theory,
        experimental results, and comparative metrics include:
        
            * `Alexis Pietak`_ and `Michael Levin`_, 2017. |2017 article name|_
              |2017 article supplement|_ [#supplement]_ |2017 journal name|_ *14*\ (134),
              p.20170425. :sup:`https://doi.org/10.1098/rsif.2017.0425`
            * Vaibhav P. Pai, `Alexis Pietak`_, Valerie Willocq, Bin Ye, Nian-Qing Shi,
              and `Michael Levin`_, 2018. |2018 hcn2 article name|_ |2018 hcn2 article
              supplement|_ [#supplement]_ |2018 hcn2 journal name|_ *9*\ (1), p.998.
              :sup:`https://doi.org/10.1038/s41467-018-03334-5`
            * Javier Cervera, `Alexis Pietak`_, `Michael Levin`_, and Salvador Mafe,
              2018. |2018 coupling article name|_ |2018 coupling journal name|_ *128*,
              pp.45—61. :sup:`https://doi.org/10.1016/j.bioelechem.2018.04.013`
            * `Alexis Pietak`_ and `Michael Levin`_, 2018. |2018 review article name|_
              |2018 review journal name|_
              :sup:`https://doi.org/10.1016/j.pbiomolbio.2018.03.008`
        
        .. # FIXME: Add an image thumbnail for the first article above displaying the
        .. # cover image selected by the prior journal for that edition's cover article.
        
        .. # Note that, for unknown reasons, this footnote *MUST* be refenced above and
        .. # defined here rather than in the supplement replacements defined below.
        
        .. [#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.
        
        Contact
        =======
        
        To contact `Dr. Pietak`_, the principal developer of the BETSE codebase and
        first or second author of all above papers, cordially direct correspondence to
        either:
        
        * The `anonymous contact form <Organic Mechanics Contact_>`__ at `Organic
          Mechanics`_, the personal archives of all material published to date by
          `Dr. Pietak`_ – including papers, presentations, textbooks, and additional
          theoretical work.
        * The personal e-mail account of `Dr. Pietak`_: [#e-mail]_
        
          * *Username:* **alexis** ``{dot}`` **pietak**
          * *Hostname:* **gmail** ``{dot}`` **com**
        
        To report a software issue (e.g., bug, crash, or other unexpected behaviour)
        *or* request a new feature in BETSE, consider `submitting a new issue <issue
        submission_>`__ to our `issue tracker`_. Thanks in advance; it's only through
        generous user contributions that your user experience can continue to improve.
        
        .. [#e-mail]
           To protect Dr. Pietak's e-mail address against `automated harvesting <e-mail
           harvesting_>`__, this address has been intentionally obfuscated. Reconstruct
           the original address by:
        
           * Replacing the ``{dot}`` substring with the ``.`` charecter.
           * Concatenating the username and hostname strings with the ``@`` character.
        
           For this reason, consider directing correspondence to the `anonymous contact
           form <Organic Mechanics Contact_>`__ at `Organic Mechanics`_ instead.
        
        Authors
        =======
        
        BETSE 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.**
        
        See Also
        ========
        
        For prospective users:
        
        -  `Installation <dependencies_>`__, detailing BETSE's installation with
           exhaustive platform-specific instructions.
        
        For prospective contributors:
        
        -  `Development <doc/md/DEVELOP.md>`__, detailing development of the BETSE
           codebase – philosophy, workflow, and otherwise.
        -  `Testing <doc/md/TEST.md>`__, detailing testing of the BETSE codebase –
           `continuous integration`_, manual testing, and otherwise.
        -  `Freezing <doc/md/FREEZE.md>`__, detailing conversion of the BETSE codebase
           into redistributable platform-specific executable binaries.
        
        License
        =======
        
        BETSE is open-source software `released <license_>`__ under the permissive `BSD
        2-clause license`_.
        
        The logo prominently displayed on this `project page <project_>`__ is a flat
        `Noun Project`_ icon entitled `"Cow," <Cows collection_>`__ `kindly released
        <Noun Project license_>`__ under the permissive `BSD-compatible <license
        compatibility_>`__ `CC BY 3.0 license`_ by `Maxim Kulikov`_.
        
        .. # ------------------( LINKS ~ betse                      )------------------
        .. _author list:
           doc/md/AUTHORS.md
        .. _codebase:
           https://gitlab.com/betse/betse/tree/master
        .. _conda package:
           https://anaconda.org/conda-forge/betse
        .. _contributors:
           https://gitlab.com/betse/betse/graphs/master
        .. _dependencies:
           doc/md/INSTALL.md
        .. _issue submission:
           https://gitlab.com/betse/betse/issues/new?issue%5Bassignee_id%5D=&issue%5Bmilestone_id%5D=
        .. _issue tracker:
           https://gitlab.com/betse/betse/issues
        .. _license:
           LICENSE
        .. _project:
           https://gitlab.com/betse/betse
        .. _testing:
           https://gitlab.com/betse/betse/pipelines
        .. _tarballs:
           https://gitlab.com/betse/betse/tags
        
        .. # ------------------( LINKS ~ betse : docs               )------------------
        .. _BETSE 0.4 documentation:
           https://www.dropbox.com/s/n8qfms2oks9cvv2/BETSE04_Documentation_Dec1st2016.pdf?dl=0
        .. _BETSE 0.3 documentation:
           https://www.dropbox.com/s/fsxhjpipbiog0ru/BETSE_Documentation_Nov1st2015.pdf?dl=0
        
        .. # ------------------( LINKS ~ betsee                     )------------------
        .. _BETSEE:
           https://gitlab.com/betse/betsee
        .. _BETSEE codebase:
           https://gitlab.com/betse/betsee/tree/master
        
        .. # ------------------( LINKS ~ academia                   )------------------
        .. _Michael Levin:
        .. _Levin, Michael:
           https://ase.tufts.edu/biology/labs/levin
        .. _Channelpedia:
           http://channelpedia.epfl.ch
        .. _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 ~ academia : ally            )------------------
        .. _Alexis Pietak:
        .. _Pietak, Alexis:
        .. _Dr. Pietak:
           https://www.researchgate.net/profile/Alexis_Pietak
        .. _Organic Mechanics:
           https://www.omecha.org
        .. _Organic Mechanics Contact:
           https://www.omecha.org/contact
        
        .. # ------------------( 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 ~ paper ~ 2017               )------------------
        .. |2017 article name| replace::
           **Bioelectric gene and reaction networks: computational modelling of genetic, biochemical and bioelectrical dynamics in pattern regulation.**
        .. _2017 article name:
           http://rsif.royalsocietypublishing.org/content/14/134/20170425
        
        .. |2017 article supplement| replace::
           **(**\ Supplement\ **).**
        .. _2017 article supplement:
           https://figshare.com/collections/Supplementary_material_from_Bioelectric_gene_and_reaction_networks_computational_modelling_of_genetic_biochemical_and_bioelectrical_dynamics_in_pattern_regulation_/3878404
        
        .. |2017 journal name| replace::
           *Journal of The Royal Society Interface,*
        .. _2017 journal name:
           http://rsif.royalsocietypublishing.org
        
        .. # ------------------( LINKS ~ paper ~ 2018 : hcn2        )------------------
        .. |2018 hcn2 article name| replace::
           **HCN2 rescues brain defects by enforcing endogenous voltage pre-patterns.**
        .. _2018 hcn2 article name:
           https://www.nature.com/articles/s41467-018-03334-5
        
        .. |2018 hcn2 article supplement| replace::
           **(**\ Supplement\ **).**
        .. _2018 hcn2 article supplement:
           https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-018-03334-5/MediaObjects/41467_2018_3334_MOESM1_ESM.pdf
        
        .. |2018 hcn2 journal name| replace::
           *Nature Communications.*
        .. _2018 hcn2 journal name:
           https://www.nature.com
        
        .. # ------------------( LINKS ~ paper ~ 2018 : coupling   )------------------
        .. |2018 coupling article name| replace::
           **Bioelectrical coupling in multicellular domains regulated by gap junctions: A conceptual approach.**
        .. _2018 coupling article name:
           https://www.sciencedirect.com/science/article/pii/S156753941830063X?via%3Dihub
        
        .. |2018 coupling journal name| replace::
           *Bioelectrochemistry.*
        .. _2018 coupling journal name:
           https://www.sciencedirect.com/journal/bioelectrochemistry
        
        .. # ------------------( LINKS ~ paper ~ 2018 : review     )------------------
        .. |2018 review article name| replace::
           **Bioelectrical control of positional information in development and regeneration: A review of conceptual and computational advances.**
        .. _2018 review article name:
           https://www.sciencedirect.com/science/article/pii/S0079610718300415
        
        .. |2018 review journal name| replace::
           *Progress in Biophysics and Molecular Biology.*
        .. _2018 review journal name:
           https://www.sciencedirect.com/journal/progress-in-biophysics-and-molecular-biology
        
        .. # ------------------( LINKS ~ science                    )------------------
        .. _bioelectricity:
           https://en.wikipedia.org/wiki/Bioelectromagnetics
        .. _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
        .. _enzyme activity:
           https://en.wikipedia.org/wiki/Enzyme_assay
        .. _ephaptic coupling:
           https://en.wikipedia.org/wiki/Ephaptic_coupling
        .. _epigenetics:
           https://en.wikipedia.org/wiki/Epigenetics
        .. _extracellular environment:
           https://en.wikipedia.org/wiki/Extracellular
        .. _finite volume:
           https://en.wikipedia.org/wiki/Finite_volume_method
        .. _galvanotaxis:
           https://en.wiktionary.org/wiki/galvanotaxis
        .. _gap junction:
        .. _gap junctions:
           https://en.wikipedia.org/wiki/Gap_junction
        .. _gene products:
           https://en.wikipedia.org/wiki/Gene_product
        .. _gene regulatory networks:
           https://en.wikipedia.org/wiki/Gene_regulatory_network
        .. _genetics:
           https://en.wikipedia.org/wiki/Genetics
        .. _genetic algorithms:
           https://en.wikipedia.org/wiki/Genetic_algorithm
        .. _Hodgkin-Huxley (HH) formalism:
           https://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model
        .. _local field potentials:
           https://en.wikipedia.org/wiki/Local_field_potential
        .. _membrane permeability:
           https://en.wikipedia.org/wiki/Cell_membrane
        .. _resting potential:
           https://en.wikipedia.org/wiki/Resting_potential
        .. _tight junctions:
           https://en.wikipedia.org/wiki/Tight_junction
        .. _transmembrane voltage:
           https://en.wikipedia.org/wiki/Membrane_potential
        .. _transepithelial potential:
           https://en.wikipedia.org/wiki/Transepithelial_potential_difference
        
        .. # ------------------( LINKS ~ science : ions             )------------------
        .. _anionic proteins:
           https://en.wikipedia.org/wiki/Ion#anion
        .. _bicarbonate: https://en.wikipedia.org/wiki/Bicarbonate
        .. _calcium:     https://en.wikipedia.org/wiki/Calcium_in_biology
        .. _chloride:    https://en.wikipedia.org/wiki/Chloride
        .. _hydrogen:    https://en.wikipedia.org/wiki/Hydron_(chemistry)
        .. _sodium:      https://en.wikipedia.org/wiki/Sodium_in_biology
        .. _potassium:   https://en.wikipedia.org/wiki/Potassium_in_biology
        
        .. # ------------------( LINKS ~ science : channels         )------------------
        .. _ion channel:
           https://en.wikipedia.org/wiki/Ion_channel
        .. _leak channels:
           https://en.wikipedia.org/wiki/Leak_channel
        .. _ligand-gated channels:
           https://en.wikipedia.org/wiki/Ligand-gated_ion_channel
        .. _voltage-gated ion channels:
           https://en.wikipedia.org/wiki/Voltage-gated_ion_channel
        
        .. |calcium-gated K+ channels| replace::
           Calcium-gated K\ :sup:`+` channels
        .. _calcium-gated K+ channels:
           https://en.wikipedia.org/wiki/Calcium-activated_potassium_channel
        
        .. # ------------------( LINKS ~ science : channels : type  )------------------
        .. _HCN1:   http://channelpedia.epfl.ch/ionchannels/61
        .. _HCN2:   http://channelpedia.epfl.ch/ionchannels/62
        .. _HCN4:   http://channelpedia.epfl.ch/ionchannels/64
        .. _Kir2.1: http://channelpedia.epfl.ch/ionchannels/42
        .. _Kv1.1:  http://channelpedia.epfl.ch/ionchannels/1
        .. _Kv1.2:  http://channelpedia.epfl.ch/ionchannels/2
        .. _Kv1.5:  http://channelpedia.epfl.ch/ionchannels/5
        .. _Kv3.3:  http://channelpedia.epfl.ch/ionchannels/13
        .. _Kv3.4:  http://channelpedia.epfl.ch/ionchannels/14
        .. _Nav1.2: http://channelpedia.epfl.ch/ionchannels/121
        .. _Nav1.3: http://channelpedia.epfl.ch/ionchannels/122
        .. _Nav1.6: http://channelpedia.epfl.ch/ionchannels/125
        .. _L-type Ca:   http://channelpedia.epfl.ch/ionchannels/212
        .. _T-type Ca:   https://en.wikipedia.org/wiki/T-type_calcium_channel
        
        .. |P/Q-type Ca| replace:: :sup:`P`\ /\ :sub:`Q`-type Ca
        .. _P/Q-type Ca:
           http://channelpedia.epfl.ch/ionchannels/78
        
        .. # ------------------( LINKS ~ science : pumps : type     )------------------
        .. _ion pumps:
           https://en.wikipedia.org/wiki/Active_transport
        
        .. # ------------------( LINKS ~ science : pumps : type     )------------------
        .. _V-ATPase: https://en.wikipedia.org/wiki/V-ATPase
        
        .. |Ca2+-ATPase| replace:: Ca\ :sup:`2+`-ATPase
        .. _Ca2+-ATPase: https://en.wikipedia.org/wiki/Calcium_ATPase
        
        .. |H+/K+-ATPase| replace:: H\ :sup:`+`/K\ :sup:`+`-ATPase
        .. _H+/K+-ATPase: https://en.wikipedia.org/wiki/Hydrogen_potassium_ATPase
        
        .. |Na+/K+-ATPase| replace:: Na\ :sup:`+`/K\ :sup:`+`-ATPase
        .. _Na+/K+-ATPase: https://en.wikipedia.org/wiki/Na%2B/K%2B-ATPase
        
        .. # ------------------( LINKS ~ science : computer         )------------------
        .. _Big Data:
           https://en.wikipedia.org/wiki/Big_data
        .. _comma-separated values:
           https://en.wikipedia.org/wiki/Comma-separated_values
        .. _continuous integration:
           https://en.wikipedia.org/wiki/Continuous_integration
        .. _directed graphs:
           https://en.wikipedia.org/wiki/Directed_graph
        .. _e-mail harvesting:
           https://en.wikipedia.org/wiki/Email_address_harvesting
        .. _genenic algorithms:
           https://en.wikipedia.org/wiki/Genetic_algorithm
        .. _knowledge-based systems:
           https://en.wikipedia.org/wiki/Knowledge-based_systems
        
        .. # ------------------( LINKS ~ os : linux                 )------------------
        .. _APT:
           https://en.wikipedia.org/wiki/Advanced_Packaging_Tool
        .. _POSIX:
           https://en.wikipedia.org/wiki/POSIX
        .. _Ubuntu:
        .. _Ubuntu Linux:
           https://www.ubuntu.com
        .. _Ubuntu Linux 16.04 (Xenial Xerus):
           http://releases.ubuntu.com/16.04
        
        .. # ------------------( LINKS ~ os : macos                 )------------------
        .. _Homebrew:
           http://brew.sh
        .. _MacPorts:
           https://www.macports.org
        
        .. # ------------------( 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
        .. _Atom:
           https://atom.io
        .. _dill:
           https://pypi.python.org/pypi/dill
        .. _FFmpeg:
           https://ffmpeg.org
        .. _Git:
           https://git-scm.com/downloads
        .. _GitLab-CI:
           https://about.gitlab.com/gitlab-ci
        .. _Graphviz:
           http://www.graphviz.org
        .. _imageio:
           https://imageio.github.io
        .. _Libav:
           https://libav.org
        .. _Matplotlib:
           http://matplotlib.org
        .. _NumPy:
           http://www.numpy.org
        .. _MEncoder:
           https://en.wikipedia.org/wiki/MEncoder
        .. _Python 3:
           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 : pyside2         )------------------
        .. _PySide2:
           https://wiki.qt.io/PySide2
        .. _PySide2 5.6:
           https://code.qt.io/cgit/pyside/pyside.git/log/?h=5.6
        .. _PySide2 installation:
           https://wiki.qt.io/PySide2_GettingStarted
        .. _PySide2 PPA:
           https://launchpad.net/~thopiekar/+archive/ubuntu/pyside-git
        .. _Qt:
           https://www.qt.io
        .. _Qt 5.6:
           https://wiki.qt.io/Qt_5.6_Release
        
        .. # ------------------( LINKS ~ software : icons           )------------------
        .. _Cows collection:
           https://thenounproject.com/maxim221/collection/cows
        .. _Maxim Kulikov:
           https://thenounproject.com/maxim221
        .. _Noun Project:
           https://thenounproject.com
        .. _Noun Project license:
           https://thenounproject.com/legal
        
        .. # ------------------( 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
        
Keywords: biology,multiphysics,science,simulator
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
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
