| Name | betse JSON |
| Version |
1.4.1
JSON |
| download |
| home_page | None |
| Summary | The BioElectric Tissue Simulation Engine (BETSE) is a discrete exterior calculus simulator for 2D computational multiphysics problems in the life sciences -- including (electro)diffusion, (electro)osmosis, galvanotaxis, voltage-gated ion channels, gene regulatory networks, and biochemical reaction networks. |
| upload_time | 2024-09-24 05:59:12 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.11 |
| license | Copyright 2014-2025 by Alexis Pietak & Cecil Curry. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
| keywords |
biology
multiphysics
science
simulator
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
.. # ------------------( 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 is
.. # thus 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 `discrete exterior calculus`_ 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 `portably implemented <codebase_>`__ in pure `Python 3`_,
`continuously stress-tested <testing_>`__ via `GitHub Actions`_ **×** tox_ **×**
pytest_ **×** Codecov_, and `permissively distributed <license_>`__ under the
`BSD 2-clause license`_.
.. # ------------------( 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 is universally installable with either:
- [\ *Recommended*\ ] pip_, the standard Python package manager:
.. code-block:: console
pip install betse
- Anaconda_, a third-party Python package manager:
.. code-block:: console
conda config --add channels conda-forge
conda install betse
See our `installation instructions <install_>`__ for details, including best
practices for `Linux <install Linux>`__, `macOS <install macOS>`__, and
`Windows usage <install Windows>`__, `Git-based development <install
developers_>`__, and `Docker-based containerization <install Docker_>`__.
Usage
=====
BETSE installs the ``betse`` command, a low-level command line interface (CLI)
ideal for advanced users.
BETSEE_ installs the ``betsee`` command, a high-level graphical user interface
(GUI) ideal for *all* users – regardless of prior experience or familiarity
with the command line.
Subcommands
-----------
The ``betse`` command accepts numerous **subcommands** (i.e., passed arguments
indicating actions to be performed).
Try
~~~
The ``try`` subcommand creates a default simulation in the current directory
and runs all requisite and optional phases of this simulation:
.. code-block:: console
betse -v try
This subcommand is typically run as an initial `smoke test`_ verifying that
BETSE was installed properly and operates as advertised. Specifically, this
subcommand:
- 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.
Seed, Init, and Sim
~~~~~~~~~~~~~~~~~~~
The ``seed``, ``init``, and ``sim`` subcommands run only the seed,
initialization, and simulation phases (respectively) for the passed simulation.
While the higher-level ``try`` subcommand conveniently runs *all* simulation
phases, it's often preferable to run only a single phase – particularly when
experimenting with computationally expensive simulations.
A typical CLI-based workflow calls these subcommands in order:
#. 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_>`__.
#. Seed (i.e., create) a pseudo-random cell cluster from this 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 seed.
.. code-block:: console
betse plot seed my_sim/sim_config.yml
#. Initialize (i.e., calculate steady-state concentrations for) this seeded
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 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
Options
-------
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] [--headless]
{config,seed,init,sim,sim-grn,plot,info,try} ...
The BioElectric Tissue Simulation Engine (BETSE) is a discrete exterior
calculus simulator for 2D computational multiphysics problems in the life
sciences -- including (electro)diffusion, (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
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")
--headless enable headless mode (display no plots or animations)
[forces "--matplotlib-backend=agg"]
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 1.0 documentation`_. (\ *PDF format; 75 pages.*\ )
- Official `BETSE 0.4 documentation`_. (\ *PDF format; 72 pages.*\ )
- Official `BETSE 0.3 documentation`_. (\ *PDF format; 77 pages.*\ )
Tutorials
---------
BETSE provides a range of `hands-on tutorial materials <tutorial user_>`__,
including simulation files to run key published simulations, as well as a
`Developer's Tutorial <tutorial dev_>`__ demonstrating how to load and work
with BETSE modules, methods, and simulations in external code projects:
- Official `BETSE Tutorial Simulation Packages <tutorial user_>`__. (\ *YAML
format.*\ )
- Official `BETSE Developer's Tutorial <tutorial dev_>`__. (\ *Jupyter
Notebook format.*\ )
Science
============
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`
* `Alexis Pietak`_, Johanna Bischof, Joshua LaPalme, Junji Morokuma, and
`Michael Levin`_, 2019. |2019 article name|_ |2019 journal name|_
:sup:`https://doi.org/10.1371/journal.pcbi.1006904`
.. # 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
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.
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.**
Funding
=======
BETSE is currently independently financed as a volunteer open-source project.
Prior grant funding sources include (in chronological order):
#. For the five-year period spanning 2015—2019, BETSE was graciously 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`_.
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`_.
See Also
========
For prospective users:
- `Installation <install_>`__, 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.
.. # ------------------( LINKS ~ betse )------------------
.. _codebase:
https://gitlab.com/betse/betse/tree/master
.. _conda package:
https://anaconda.org/conda-forge/betse
.. _contributors:
https://gitlab.com/betse/betse/graphs/master
.. _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
.. _project:
https://gitlab.com/betse/betse
.. _tarballs:
https://gitlab.com/betse/betse/tags
.. # ------------------( LINKS ~ betse : ci )------------------
.. _Appveyor:
https://ci.appveyor.com/project/betse/betse/branch/master
.. _testing:
https://gitlab.com/betse/betse/pipelines
.. # ------------------( LINKS ~ betse : docs )------------------
.. _BETSE 1.0 documentation:
https://www.dropbox.com/s/3rsbrjq2ljal8dl/BETSE_Documentation_April10th2019.pdf?dl=0
.. _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 ~ betse : local )------------------
.. _author list:
doc/md/AUTHORS.md
.. _license:
LICENSE
.. # ------------------( LINKS ~ betse : local : install )------------------
.. _install:
doc/rst/INSTALL.rst
.. _install developers:
doc/rst/INSTALL.rst#developers
.. _install Docker:
doc/rst/INSTALL.rst#docker
.. _install Linux:
doc/rst/INSTALL.rst#linux
.. _install macOS:
doc/rst/INSTALL.rst#macos
.. _install Windows:
doc/rst/INSTALL.rst#windows
.. # ------------------( LINKS ~ betse : local : tutorial )------------------
.. _tutorial dev:
doc/md/DEV_DEMO.md
.. _tutorial user:
doc/md/TUTORIALS.md
.. # ------------------( 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 ~ paper ~ 2019 )------------------
.. |2019 article name| replace::
**Neural control of body-plan axis in regenerating planaria.**
.. _2019 article name:
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006904
.. |2019 journal name| replace::
*PLOS Computational Biology.*
.. _2019 journal name:
https://journals.plos.org/ploscompbiol
.. # ------------------( LINKS ~ science )------------------
.. _bioelectricity:
https://en.wikipedia.org/wiki/Bioelectromagnetics
.. _biochemical reaction networks:
http://www.nature.com/subjects/biochemical-reaction-networks
.. _discrete exterior calculus:
https://en.wikipedia.org/wiki/Discrete_exterior_calculus
.. _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
.. _smoke test:
https://en.wikipedia.org/wiki/Smoke_testing_(software)
.. # ------------------( 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 ~ soft )------------------
.. _Atom:
https://atom.io
.. _FFmpeg:
https://ffmpeg.org
.. _Git:
https://git-scm.com/downloads
.. _Graphviz:
http://www.graphviz.org
.. _Libav:
https://libav.org
.. _MEncoder:
https://en.wikipedia.org/wiki/MEncoder
.. _VirtualBox:
https://www.virtualbox.org
.. _YAML:
http://yaml.org
.. # ------------------( LINKS ~ soft : github )------------------
.. _GitHub Actions:
https://github.com/features/actions
.. # ------------------( LINKS ~ soft : icon )------------------
.. _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 ~ soft : license )------------------
.. _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
.. # ------------------( LINKS ~ soft : py )------------------
.. _dill:
https://pypi.python.org/pypi/dill
.. _imageio:
https://imageio.github.io
.. _Matplotlib:
http://matplotlib.org
.. _NumPy:
http://www.numpy.org
.. _PyPI:
https://pypi.python.org
.. _Python:
.. _Python 3:
https://www.python.org
.. _pip:
https://pip.pypa.io
.. _SciPy:
http://www.scipy.org
.. # ------------------( LINKS ~ soft : py : conda )------------------
.. _Anaconda:
https://www.anaconda.com/download
.. _Anaconda packages:
https://anaconda.org
.. _conda-forge:
https://conda-forge.org
.. # ------------------( LINKS ~ soft : py : package : test )------------------
.. _Codecov:
https://about.codecov.io
.. _pytest:
https://docs.pytest.org
.. _tox:
https://tox.readthedocs.io
.. # ------------------( LINKS ~ soft : py : package : pys2 )------------------
.. _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
Raw data
{
"_id": null,
"home_page": null,
"name": "betse",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.11",
"maintainer_email": "Cecil Curry <leycec@gmail.com>",
"keywords": "biology, multiphysics, science, simulator",
"author": null,
"author_email": "Alexis Pietak <alexis.pietak@gmail.com>",
"download_url": "https://files.pythonhosted.org/packages/42/12/67e2f0b58d19945a8235575d6aafeb2c4b51c37fbda5a8fde29ff206c6f8/betse-1.4.1.tar.gz",
"platform": null,
"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 is\n.. # thus disabled until more widely supported. *collective shrug*\n.. # highlight:: console\n\n.. # ------------------( SYNOPSIS )------------------\n\n=====\nBETSE\n=====\n\n**BETSE** (**B**\\ io\\ **E**\\ lectric **T**\\ issue **S**\\ imulation **E**\\\nngine) is an open-source cross-platform `discrete exterior calculus`_ simulator\nfor 2D computational multiphysics problems in the life sciences \u2013 including\nelectrodiffusion_, electro-osmosis_, galvanotaxis_, `voltage-gated ion\nchannels`_, `gene regulatory networks`_, and `biochemical reaction networks`_\n(e.g., metabolism).\n\nBETSE is `portably implemented <codebase_>`__ in pure `Python 3`_,\n`continuously stress-tested <testing_>`__ via `GitHub Actions`_ **\u00d7** tox_ **\u00d7**\npytest_ **\u00d7** Codecov_, and `permissively distributed <license_>`__ 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\nBETSE is universally installable with either:\n\n- [\\ *Recommended*\\ ] pip_, the standard Python package manager:\n\n .. code-block:: console\n\n pip install betse\n\n- Anaconda_, a third-party Python package manager:\n\n .. code-block:: console\n\n conda config --add channels conda-forge\n conda install betse\n\nSee our `installation instructions <install_>`__ for details, including best\npractices for `Linux <install Linux>`__, `macOS <install macOS>`__, and\n`Windows usage <install Windows>`__, `Git-based development <install\ndevelopers_>`__, and `Docker-based containerization <install Docker_>`__.\n\nUsage\n=====\n\nBETSE installs the ``betse`` command, a low-level command line interface (CLI)\nideal for advanced users.\n\nBETSEE_ installs the ``betsee`` command, a high-level graphical user interface\n(GUI) ideal for *all* users \u2013 regardless of prior experience or familiarity\nwith the command line.\n\nSubcommands\n-----------\n\nThe ``betse`` command accepts numerous **subcommands** (i.e., passed arguments\nindicating actions to be performed).\n\nTry\n~~~\n\nThe ``try`` subcommand creates a default simulation in the current directory\nand runs all requisite and optional phases of this simulation:\n\n.. code-block:: console\n\n betse -v try\n\nThis subcommand is typically run as an initial `smoke test`_ verifying that\nBETSE was installed properly and operates as advertised. Specifically, this\nsubcommand:\n\n- Enables verbosity with the ``-v`` option, simplifying issue reporting in the\n event of an unexpected error.\n- Creates a ``sample_sim/`` subdirectory in the current directory, providing\n the default simulation for this release of BETSE. This includes *all*\n configuration files and resources referenced by these files.\n- Runs all simulation phases (e.g., seed, initialization) of this simulation.\n\nWhen finished, you may safely either:\n\n+ Remove this subdirectory.\n+ Rename this subdirectory (e.g., to ``my_sim/``) to serve as a basis for\n subsequent simulations.\n+ Preserve this subdirectory as is.\n\nSeed, Init, and Sim\n~~~~~~~~~~~~~~~~~~~\n\nThe ``seed``, ``init``, and ``sim`` subcommands run only the seed,\ninitialization, and simulation phases (respectively) for the passed simulation.\nWhile the higher-level ``try`` subcommand conveniently runs *all* simulation\nphases, it's often preferable to run only a single phase \u2013 particularly when\nexperimenting with computationally expensive simulations.\n\nA typical CLI-based workflow calls these subcommands in order:\n\n#. Create a default simulation configuration in a new ``my_sim/`` subdirectory\n of the current directory.\n\n .. code-block:: console\n\n betse config my_sim/sim_config.yml\n\n#. [\\ *Optional*\\ ] Edit the new ``my_sim/sim_config.yml`` file with `your\n favourite text editor <Atom_>`__.\n#. Seed (i.e., create) a pseudo-random cell cluster from this configuration.\n\n .. code-block:: console\n\n betse seed my_sim/sim_config.yml\n\n#. [\\ *Optional*\\ ] Export all enabled plots, animations, and comma-separated\n value (CSV) files from this seed.\n\n .. code-block:: console\n\n betse plot seed my_sim/sim_config.yml\n\n#. Initialize (i.e., calculate steady-state concentrations for) this seeded\n cluster.\n\n .. code-block:: console\n\n betse init my_sim/sim_config.yml\n\n#. [\\ *Optional*\\ ] Export all enabled plots, animations, and comma-separated\n value (CSV) files from this initialization.\n\n .. code-block:: console\n\n betse plot init my_sim/sim_config.yml\n\n#. Simulate this initialized cluster.\n\n .. code-block:: console\n\n betse sim my_sim/sim_config.yml\n\n#. [\\ *Optional*\\ ] Export all enabled plots, animations, and comma-separated\n value (CSV) files from this simulation.\n\n .. code-block:: console\n\n betse plot sim my_sim/sim_config.yml\n\nOptions\n-------\n\nBETSE provides a variety of command-line options and subcommands in addition to\nthose synopsized above. The standalone ``betse`` and ``betse --help`` commands\ndescribe these options and subcommands as follows:\n\n.. code-block:: console\n\n usage: betse [-h] [-v] [-V] [--log-file LOG_FILENAME]\n [--log-level {all,debug,info,warning,error,critical,none}]\n [--profile-type {none,call,size}]\n [--profile-file PROFILE_FILENAME]\n [--matplotlib-backend MATPLOTLIB_BACKEND_NAME] [--headless]\n {config,seed,init,sim,sim-grn,plot,info,try} ...\n \n The BioElectric Tissue Simulation Engine (BETSE) is a discrete exterior\n calculus simulator for 2D computational multiphysics problems in the life\n sciences -- including (electro)diffusion, (electro)osmosis, galvanotaxis,\n voltage-gated ion channels, gene regulatory networks, and biochemical reaction\n networks.\n \n optional arguments:\n -h, --help show this help message and exit\n -v, --verbose print and log all messages verbosely\n -V, --version print program version and exit\n --log-file LOG_FILENAME\n file to log to (defaults to\n minimum level of messages to log to \"--log-file\"\n (defaults to \"info\") [overridden by \"--verbose\"]\n --profile-type {none,call,size}\n type of profiling to perform (defaults to \"none\"):\n * \"none\", disabling profiling\n * \"call\", profiling callables (functions, methods)\n * \"size\", profiling object sizes (requires \"pympler\")\n --profile-file PROFILE_FILENAME\n file to profile to unless \"--profile-type=none\"\n (defaults to \"/home/leycec/.betse/betse.prof\")\n --matplotlib-backend MATPLOTLIB_BACKEND_NAME\n name of matplotlib backend to use (see: \"betse info\")\n --headless enable headless mode (display no plots or animations)\n [forces \"--matplotlib-backend=agg\"]\n \n subcommands:\n Exactly one of the following subcommands must be passed:\n \n {config,seed,init,sim,sim-grn,plot,info,try}\n config create a default config file for BETSE simulations\n seed seed a new cell cluster for a config file\n init initialize a seeded cell cluster for a config file\n sim simulate an initialized cell cluster for a config file\n sim-grn simulate a gene regulatory network for a config file\n plot plot an initialized or simulated simulation\n info print metadata synopsizing BETSE and current system\n try create, init, simulate, and plot a sample simulation\n \n subcommand help:\n \n For help with a specific subcommand, pass the \"-h\" or \"--help\" option to that\n subcommand. For example, for help with the \"config\" subcommand, run:\n \n betse config --help\n\nDocumentation\n-------------\n\nBETSE also provides external documentation optimized for offline reading \u2013\ncomplete with explanatory examples, sample plots, and ample screenshots:\n\n- Official `BETSE 1.0 documentation`_. (\\ *PDF format; 75 pages.*\\ )\n- Official `BETSE 0.4 documentation`_. (\\ *PDF format; 72 pages.*\\ )\n- Official `BETSE 0.3 documentation`_. (\\ *PDF format; 77 pages.*\\ )\n\nTutorials\n---------\n\nBETSE provides a range of `hands-on tutorial materials <tutorial user_>`__,\nincluding simulation files to run key published simulations, as well as a\n`Developer's Tutorial <tutorial dev_>`__ demonstrating how to load and work\nwith BETSE modules, methods, and simulations in external code projects:\n\n- Official `BETSE Tutorial Simulation Packages <tutorial user_>`__. (\\ *YAML\n format.*\\ )\n- Official `BETSE Developer's Tutorial <tutorial dev_>`__. (\\ *Jupyter\n Notebook format.*\\ )\n\nScience\n============\n\nBETSE simulates biorealistic electrochemical phenomena in `gap junction`_\\\n-networked 2D cellular collectives. To predict `bioelectric patterns\n<bioelectricity_>`__ and their spatio-temporal dynamics, BETSE:\n\n- Models `ion channel`_ and `gap junction`_ activity.\n- Tracks changes in ion concentration and net ionic charge.\n- Calculates endogenous voltages and currents.\n- Accepts simulation parameters, variables, and options as human-readable,\n well-commented configuration files in YAML_ format.\n- Exports simulation results to a variety of output formats, including:\n\n - Publication-quality:\n\n - Plots, charts, and animations driven by Matplotlib_, the industry\n standard for open-source plot visualization.\n - `Directed graphs`_ (i.e., networks) driven by Graphviz_, the industry\n standard for open-source graph visualization.\n\n - Internet-friendly compressed video driven by any of various popular\n open-source video encoders, including FFmpeg_, Libav_, and MEncoder_.\n - Post-processable tabular data (e.g., `comma-separated values (CSV)\n <comma-separated values_>`__).\n\n- Imports bitmask images defining the shapes of:\n\n - Cell clusters.\n - Cell cluster regions localizing `ion channel`_ activity, typically\n signifying disparate types of adjacent tissue.\n\nTo assemble simple concepts into complex simulations, BETSE supplies a richly\nconfigurable, highly scalable biological toolset consisting of:\n\nIons\n----\n\nSimulations may enable arbitrary combinations of the principal ions implicated\nin bioelectrical signaling \u2013 including:\n\n- Sodium_ (*Na*\\ :sup:`+`).\n- Potassium_ (*K*\\ :sup:`+`).\n- Chloride_ (*Cl*\\ :sup:`-`).\n- Calcium_ (*Ca*\\ :sup:`2+`).\n- Hydrogen_ (*H*\\ :sup:`+`).\n- `Anionic proteins`_ (*P*\\ :sup:`-`).\n- Bicarbonate_ (*HCO*\\ :sup:`-`\\ :sub:`3`).\n\nIon Channels\n------------\n\nIndividual cells in simulations may enable arbitrary combinations of\n`voltage-gated ion channels`_, each implementing the `Hodgkin-Huxley (HH)\nformalism`_ with experimentally-derived parameters sourced from reputable\n`knowledge-based systems`_ (e.g., Channelpedia_). Explicitly supported channel\ntypes include:\n\n- HCN1_, HCN2_, and HCN4_.\n- `L-type Ca`_, `T-type Ca`_, and |P/Q-type Ca|_.\n- Kir2.1_.\n- Kv1.1_, Kv1.2_, Kv1.5_. Kv3.3_, and Kv3.4_.\n- Nav1.2_, Nav1.3_, and Nav1.6_.\n- `Leak <leak channels_>`__ and `ligand-gated channels`_, including:\n\n - |Calcium-gated K+ channels|_.\n\nCustom ion channels parametrized by user-selected constants may be trivially\ndefined in the same manner (e.g., via a YAML_\\ -formatted configuration file).\n\nIon Pumps and Exchangers\n------------------------\n\nFor fine-grained control over cell dynamics, notable ion pumps and exchangers\nmay also be selectively enabled \u2013 including:\n\n- |Ca2+-ATPase|_.\n- |H+/K+-ATPase|_.\n- |Na+/K+-ATPase|_.\n- V-ATPase_.\n\nCustom ion pumps and exchangers parametrized by user-selected constants may be\ntrivially defined in the same manner (e.g., via a YAML_\\ -formatted\nconfiguration file).\n\nExtracellular Space\n-------------------\n\nCells form interconnected intracellular networks via voltage-sensitive `gap\njunction connections <gap junction_>`__ embedded within an `extracellular\nenvironment`_, maintained by `tight junctions`_ at the cell cluster periphery.\nSimulation of this environment enables exploration of `local field\npotentials`_, `transepithelial potential`_, and `ephaptic coupling`_ between\ncells.\n\nBiological Networks\n-------------------\n\nSimulation of `gene regulatory <gene regulatory networks_>`__ and `biochemical\nreaction networks`_ at both the cellular and mitochondrial level supports deep\nspatial analysis of otherwise intractable biological processes. Metabolism,\ndisease, aging, and other `genetic <genetics_>`__ and `epigenetic\n<epigenetics_>`__ phenomena commonly associated with quasi-`Big Data`_ are all\nvalid targets for exhaustive study with BETSE.\n\nTo integrate these potent control systems with bioelectrical signaling, the\n`activity <enzyme activity_>`__-modulated interaction between `gene products`_\nand similar biochemicals is fully integrated with `ion channels <ion\nchannel_>`__, `ion pumps`_, and `gap junctions`_.\n\nValidation\n----------\n\nBETSE is peer-reviewed software receiving continual evidence-based scrutiny.\nSimulation output is reproducibly synchronized with experimental observations on\n`membrane permeability`_, `resting potential`_, ion concentration, and similar\nreal-world biophysical quantities. Predictable outcomes have been demonstrated\nfor such well-known cases as:\n\n- `Transmembrane voltage changes <transmembrane voltage_>`__ on perturbations\n to single cell membrane states and environmental ion concentrations.\n- `Transepithelial potential differences (TEPD) <transepithelial\n potential_>`__.\n- Bioelectrical signals at large-scale cellular wound sites.\n\nCitation\n========\n\nBETSE is formally described in our `introductory paper <2016 article_>`__.\nThird-party papers, theses, and other texts leveraging BETSE should ideally\ncite 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\nSubsequent papers expanding the BETSE architecture with additional theory,\nexperimental results, and comparative metrics include:\n\n * `Alexis Pietak`_ and `Michael Levin`_, 2017. |2017 article name|_\n |2017 article supplement|_ [#supplement]_ |2017 journal name|_ *14*\\ (134),\n p.20170425. :sup:`https://doi.org/10.1098/rsif.2017.0425`\n * Vaibhav P. Pai, `Alexis Pietak`_, Valerie Willocq, Bin Ye, Nian-Qing Shi,\n and `Michael Levin`_, 2018. |2018 hcn2 article name|_ |2018 hcn2 article\n supplement|_ [#supplement]_ |2018 hcn2 journal name|_ *9*\\ (1), p.998.\n :sup:`https://doi.org/10.1038/s41467-018-03334-5`\n * Javier Cervera, `Alexis Pietak`_, `Michael Levin`_, and Salvador Mafe,\n 2018. |2018 coupling article name|_ |2018 coupling journal name|_ *128*,\n pp.45\u201461. :sup:`https://doi.org/10.1016/j.bioelechem.2018.04.013`\n * `Alexis Pietak`_ and `Michael Levin`_, 2018. |2018 review article name|_\n |2018 review journal name|_\n :sup:`https://doi.org/10.1016/j.pbiomolbio.2018.03.008`\n * `Alexis Pietak`_, Johanna Bischof, Joshua LaPalme, Junji Morokuma, and\n `Michael Levin`_, 2019. |2019 article name|_ |2019 journal name|_\n :sup:`https://doi.org/10.1371/journal.pcbi.1006904`\n\n.. # FIXME: Add an image thumbnail for the first article above displaying the\n.. # cover image selected by the prior journal for that edition's cover article.\n\n.. # Note that, for unknown reasons, this footnote *MUST* be refenced above and\n.. # defined here rather than in the supplement replacements defined below.\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\nContact\n=======\n\nTo contact `Dr. Pietak`_, the principal developer of the BETSE codebase and\nfirst or second author of all above papers, cordially direct correspondence to\nthe personal e-mail account of `Dr. Pietak`_: [#e-mail]_\n\n* *Username:* **alexis** ``{dot}`` **pietak**\n* *Hostname:* **gmail** ``{dot}`` **com**\n\nTo report a software issue (e.g., bug, crash, or other unexpected behaviour)\n*or* request a new feature in BETSE, consider `submitting a new issue <issue\nsubmission_>`__ to our `issue tracker`_. Thanks in advance; it's only through\ngenerous user contributions that your user experience can continue to improve.\n\n.. [#e-mail]\n To protect Dr. Pietak's e-mail address against `automated harvesting <e-mail\n harvesting_>`__, this address has been intentionally obfuscated. Reconstruct\n the original address by:\n\n * Replacing the ``{dot}`` substring with the ``.`` charecter.\n * Concatenating the username and hostname strings with the ``@`` character.\n\nAuthors\n=======\n\nBETSE comes courtesy a dedicated community of `authors <author list_>`__ and\ncontributors_ \u2013 without whom this project would be computationally impoverished,\nbiologically misaligned, and simply unusable.\n\n**Thanks, all.**\n\nFunding\n=======\n\nBETSE is currently independently financed as a volunteer open-source project.\nPrior grant funding sources include (in chronological order):\n\n#. For the five-year period spanning 2015\u20142019, BETSE was graciously associated\n with the `Paul Allen Discovery Center`_ at `Tufts University`_ and supported\n by a `Paul Allen Discovery Center award`_ from the `Paul G. Allen Frontiers\n Group`_.\n\nLicense\n=======\n\nBETSE is open-source software `released <license_>`__ under the permissive `BSD\n2-clause license`_.\n\nThe logo prominently displayed on this `project page <project_>`__ is a flat\n`Noun Project`_ icon entitled `\"Cow,\" <Cows collection_>`__ `kindly released\n<Noun Project license_>`__ under the permissive `BSD-compatible <license\ncompatibility_>`__ `CC BY 3.0 license`_ by `Maxim Kulikov`_.\n\nSee Also\n========\n\nFor prospective users:\n\n- `Installation <install_>`__, detailing BETSE's installation with exhaustive\n platform-specific instructions.\n\nFor prospective contributors:\n\n- `Development <doc/md/DEVELOP.md>`__, detailing development of the BETSE\n codebase \u2013 philosophy, workflow, and otherwise.\n- `Testing <doc/md/TEST.md>`__, detailing testing of the BETSE codebase \u2013\n `continuous integration`_, manual testing, and otherwise.\n- `Freezing <doc/md/FREEZE.md>`__, detailing conversion of the BETSE codebase\n into redistributable platform-specific executable binaries.\n\n.. # ------------------( LINKS ~ betse )------------------\n.. _codebase:\n https://gitlab.com/betse/betse/tree/master\n.. _conda package:\n https://anaconda.org/conda-forge/betse\n.. _contributors:\n https://gitlab.com/betse/betse/graphs/master\n.. _issue submission:\n https://gitlab.com/betse/betse/issues/new?issue%5Bassignee_id%5D=&issue%5Bmilestone_id%5D=\n.. _issue tracker:\n https://gitlab.com/betse/betse/issues\n.. _project:\n https://gitlab.com/betse/betse\n.. _tarballs:\n https://gitlab.com/betse/betse/tags\n\n.. # ------------------( LINKS ~ betse : ci )------------------\n.. _Appveyor:\n https://ci.appveyor.com/project/betse/betse/branch/master\n.. _testing:\n https://gitlab.com/betse/betse/pipelines\n\n.. # ------------------( LINKS ~ betse : docs )------------------\n.. _BETSE 1.0 documentation:\n https://www.dropbox.com/s/3rsbrjq2ljal8dl/BETSE_Documentation_April10th2019.pdf?dl=0\n.. _BETSE 0.4 documentation:\n https://www.dropbox.com/s/n8qfms2oks9cvv2/BETSE04_Documentation_Dec1st2016.pdf?dl=0\n.. _BETSE 0.3 documentation:\n https://www.dropbox.com/s/fsxhjpipbiog0ru/BETSE_Documentation_Nov1st2015.pdf?dl=0\n\n.. # ------------------( LINKS ~ betse : local )------------------\n.. _author list:\n doc/md/AUTHORS.md\n.. _license:\n LICENSE\n\n.. # ------------------( LINKS ~ betse : local : install )------------------\n.. _install:\n doc/rst/INSTALL.rst\n.. _install developers:\n doc/rst/INSTALL.rst#developers\n.. _install Docker:\n doc/rst/INSTALL.rst#docker\n.. _install Linux:\n doc/rst/INSTALL.rst#linux\n.. _install macOS:\n doc/rst/INSTALL.rst#macos\n.. _install Windows:\n doc/rst/INSTALL.rst#windows\n\n.. # ------------------( LINKS ~ betse : local : tutorial )------------------\n.. _tutorial dev:\n doc/md/DEV_DEMO.md\n.. _tutorial user:\n doc/md/TUTORIALS.md\n\n.. # ------------------( LINKS ~ betsee )------------------\n.. _BETSEE:\n https://gitlab.com/betse/betsee\n.. _BETSEE codebase:\n https://gitlab.com/betse/betsee/tree/master\n\n.. # ------------------( LINKS ~ academia )------------------\n.. _Michael Levin:\n.. _Levin, Michael:\n https://ase.tufts.edu/biology/labs/levin\n.. _Channelpedia:\n http://channelpedia.epfl.ch\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 ~ academia : ally )------------------\n.. _Alexis Pietak:\n.. _Pietak, Alexis:\n.. _Dr. Pietak:\n https://www.researchgate.net/profile/Alexis_Pietak\n.. _Organic Mechanics:\n https://www.omecha.org\n.. _Organic Mechanics Contact:\n https://www.omecha.org/contact\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 ~ paper ~ 2017 )------------------\n.. |2017 article name| replace::\n **Bioelectric gene and reaction networks: computational modelling of genetic, biochemical and bioelectrical dynamics in pattern regulation.**\n.. _2017 article name:\n http://rsif.royalsocietypublishing.org/content/14/134/20170425\n\n.. |2017 article supplement| replace::\n **(**\\ Supplement\\ **).**\n.. _2017 article supplement:\n https://figshare.com/collections/Supplementary_material_from_Bioelectric_gene_and_reaction_networks_computational_modelling_of_genetic_biochemical_and_bioelectrical_dynamics_in_pattern_regulation_/3878404\n\n.. |2017 journal name| replace::\n *Journal of The Royal Society Interface,*\n.. _2017 journal name:\n http://rsif.royalsocietypublishing.org\n\n.. # ------------------( LINKS ~ paper ~ 2018 : hcn2 )------------------\n.. |2018 hcn2 article name| replace::\n **HCN2 rescues brain defects by enforcing endogenous voltage pre-patterns.**\n.. _2018 hcn2 article name:\n https://www.nature.com/articles/s41467-018-03334-5\n\n.. |2018 hcn2 article supplement| replace::\n **(**\\ Supplement\\ **).**\n.. _2018 hcn2 article supplement:\n https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-018-03334-5/MediaObjects/41467_2018_3334_MOESM1_ESM.pdf\n\n.. |2018 hcn2 journal name| replace::\n *Nature Communications.*\n.. _2018 hcn2 journal name:\n https://www.nature.com\n\n.. # ------------------( LINKS ~ paper ~ 2018 : coupling )------------------\n.. |2018 coupling article name| replace::\n **Bioelectrical coupling in multicellular domains regulated by gap junctions: A conceptual approach.**\n.. _2018 coupling article name:\n https://www.sciencedirect.com/science/article/pii/S156753941830063X?via%3Dihub\n\n.. |2018 coupling journal name| replace::\n *Bioelectrochemistry.*\n.. _2018 coupling journal name:\n https://www.sciencedirect.com/journal/bioelectrochemistry\n\n.. # ------------------( LINKS ~ paper ~ 2018 : review )------------------\n.. |2018 review article name| replace::\n **Bioelectrical control of positional information in development and regeneration: A review of conceptual and computational advances.**\n.. _2018 review article name:\n https://www.sciencedirect.com/science/article/pii/S0079610718300415\n\n.. |2018 review journal name| replace::\n *Progress in Biophysics and Molecular Biology.*\n.. _2018 review journal name:\n https://www.sciencedirect.com/journal/progress-in-biophysics-and-molecular-biology\n\n.. # ------------------( LINKS ~ paper ~ 2019 )------------------\n.. |2019 article name| replace::\n **Neural control of body-plan axis in regenerating planaria.**\n.. _2019 article name:\n https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006904\n\n.. |2019 journal name| replace::\n *PLOS Computational Biology.*\n.. _2019 journal name:\n https://journals.plos.org/ploscompbiol\n\n.. # ------------------( LINKS ~ science )------------------\n.. _bioelectricity:\n https://en.wikipedia.org/wiki/Bioelectromagnetics\n.. _biochemical reaction networks:\n http://www.nature.com/subjects/biochemical-reaction-networks\n.. _discrete exterior calculus:\n https://en.wikipedia.org/wiki/Discrete_exterior_calculus\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.. _enzyme activity:\n https://en.wikipedia.org/wiki/Enzyme_assay\n.. _ephaptic coupling:\n https://en.wikipedia.org/wiki/Ephaptic_coupling\n.. _epigenetics:\n https://en.wikipedia.org/wiki/Epigenetics\n.. _extracellular environment:\n https://en.wikipedia.org/wiki/Extracellular\n.. _finite volume:\n https://en.wikipedia.org/wiki/Finite_volume_method\n.. _galvanotaxis:\n https://en.wiktionary.org/wiki/galvanotaxis\n.. _gap junction:\n.. _gap junctions:\n https://en.wikipedia.org/wiki/Gap_junction\n.. _gene products:\n https://en.wikipedia.org/wiki/Gene_product\n.. _gene regulatory networks:\n https://en.wikipedia.org/wiki/Gene_regulatory_network\n.. _genetics:\n https://en.wikipedia.org/wiki/Genetics\n.. _genetic algorithms:\n https://en.wikipedia.org/wiki/Genetic_algorithm\n.. _Hodgkin-Huxley (HH) formalism:\n https://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model\n.. _local field potentials:\n https://en.wikipedia.org/wiki/Local_field_potential\n.. _membrane permeability:\n https://en.wikipedia.org/wiki/Cell_membrane\n.. _resting potential:\n https://en.wikipedia.org/wiki/Resting_potential\n.. _tight junctions:\n https://en.wikipedia.org/wiki/Tight_junction\n.. _transmembrane voltage:\n https://en.wikipedia.org/wiki/Membrane_potential\n.. _transepithelial potential:\n https://en.wikipedia.org/wiki/Transepithelial_potential_difference\n\n.. # ------------------( LINKS ~ science : ions )------------------\n.. _anionic proteins:\n https://en.wikipedia.org/wiki/Ion#anion\n.. _bicarbonate: https://en.wikipedia.org/wiki/Bicarbonate\n.. _calcium: https://en.wikipedia.org/wiki/Calcium_in_biology\n.. _chloride: https://en.wikipedia.org/wiki/Chloride\n.. _hydrogen: https://en.wikipedia.org/wiki/Hydron_(chemistry)\n.. _sodium: https://en.wikipedia.org/wiki/Sodium_in_biology\n.. _potassium: https://en.wikipedia.org/wiki/Potassium_in_biology\n\n.. # ------------------( LINKS ~ science : channels )------------------\n.. _ion channel:\n https://en.wikipedia.org/wiki/Ion_channel\n.. _leak channels:\n https://en.wikipedia.org/wiki/Leak_channel\n.. _ligand-gated channels:\n https://en.wikipedia.org/wiki/Ligand-gated_ion_channel\n.. _voltage-gated ion channels:\n https://en.wikipedia.org/wiki/Voltage-gated_ion_channel\n\n.. |calcium-gated K+ channels| replace::\n Calcium-gated K\\ :sup:`+` channels\n.. _calcium-gated K+ channels:\n https://en.wikipedia.org/wiki/Calcium-activated_potassium_channel\n\n.. # ------------------( LINKS ~ science : channels : type )------------------\n.. _HCN1: http://channelpedia.epfl.ch/ionchannels/61\n.. _HCN2: http://channelpedia.epfl.ch/ionchannels/62\n.. _HCN4: http://channelpedia.epfl.ch/ionchannels/64\n.. _Kir2.1: http://channelpedia.epfl.ch/ionchannels/42\n.. _Kv1.1: http://channelpedia.epfl.ch/ionchannels/1\n.. _Kv1.2: http://channelpedia.epfl.ch/ionchannels/2\n.. _Kv1.5: http://channelpedia.epfl.ch/ionchannels/5\n.. _Kv3.3: http://channelpedia.epfl.ch/ionchannels/13\n.. _Kv3.4: http://channelpedia.epfl.ch/ionchannels/14\n.. _Nav1.2: http://channelpedia.epfl.ch/ionchannels/121\n.. _Nav1.3: http://channelpedia.epfl.ch/ionchannels/122\n.. _Nav1.6: http://channelpedia.epfl.ch/ionchannels/125\n.. _L-type Ca: http://channelpedia.epfl.ch/ionchannels/212\n.. _T-type Ca: https://en.wikipedia.org/wiki/T-type_calcium_channel\n\n.. |P/Q-type Ca| replace:: :sup:`P`\\ /\\ :sub:`Q`-type Ca\n.. _P/Q-type Ca:\n http://channelpedia.epfl.ch/ionchannels/78\n\n.. # ------------------( LINKS ~ science : pumps : type )------------------\n.. _ion pumps:\n https://en.wikipedia.org/wiki/Active_transport\n\n.. # ------------------( LINKS ~ science : pumps : type )------------------\n.. _V-ATPase: https://en.wikipedia.org/wiki/V-ATPase\n\n.. |Ca2+-ATPase| replace:: Ca\\ :sup:`2+`-ATPase\n.. _Ca2+-ATPase: https://en.wikipedia.org/wiki/Calcium_ATPase\n\n.. |H+/K+-ATPase| replace:: H\\ :sup:`+`/K\\ :sup:`+`-ATPase\n.. _H+/K+-ATPase: https://en.wikipedia.org/wiki/Hydrogen_potassium_ATPase\n\n.. |Na+/K+-ATPase| replace:: Na\\ :sup:`+`/K\\ :sup:`+`-ATPase\n.. _Na+/K+-ATPase: https://en.wikipedia.org/wiki/Na%2B/K%2B-ATPase\n\n.. # ------------------( LINKS ~ science : computer )------------------\n.. _Big Data:\n https://en.wikipedia.org/wiki/Big_data\n.. _comma-separated values:\n https://en.wikipedia.org/wiki/Comma-separated_values\n.. _continuous integration:\n https://en.wikipedia.org/wiki/Continuous_integration\n.. _directed graphs:\n https://en.wikipedia.org/wiki/Directed_graph\n.. _e-mail harvesting:\n https://en.wikipedia.org/wiki/Email_address_harvesting\n.. _genenic algorithms:\n https://en.wikipedia.org/wiki/Genetic_algorithm\n.. _knowledge-based systems:\n https://en.wikipedia.org/wiki/Knowledge-based_systems\n.. _smoke test:\n https://en.wikipedia.org/wiki/Smoke_testing_(software)\n\n.. # ------------------( LINKS ~ os : linux )------------------\n.. _APT:\n https://en.wikipedia.org/wiki/Advanced_Packaging_Tool\n.. _POSIX:\n https://en.wikipedia.org/wiki/POSIX\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.. # ------------------( LINKS ~ os : macos )------------------\n.. _Homebrew:\n http://brew.sh\n.. _MacPorts:\n https://www.macports.org\n\n.. # ------------------( LINKS ~ os : windows )------------------\n.. _WSL:\n https://msdn.microsoft.com/en-us/commandline/wsl/install-win10\n\n.. # ------------------( LINKS ~ soft )------------------\n.. _Atom:\n https://atom.io\n.. _FFmpeg:\n https://ffmpeg.org\n.. _Git:\n https://git-scm.com/downloads\n.. _Graphviz:\n http://www.graphviz.org\n.. _Libav:\n https://libav.org\n.. _MEncoder:\n https://en.wikipedia.org/wiki/MEncoder\n.. _VirtualBox:\n https://www.virtualbox.org\n.. _YAML:\n http://yaml.org\n\n.. # ------------------( LINKS ~ soft : github )------------------\n.. _GitHub Actions:\n https://github.com/features/actions\n\n.. # ------------------( LINKS ~ soft : icon )------------------\n.. _Cows collection:\n https://thenounproject.com/maxim221/collection/cows\n.. _Maxim Kulikov:\n https://thenounproject.com/maxim221\n.. _Noun Project:\n https://thenounproject.com\n.. _Noun Project license:\n https://thenounproject.com/legal\n\n.. # ------------------( LINKS ~ soft : license )------------------\n.. _license compatibility:\n https://en.wikipedia.org/wiki/License_compatibility#Compatibility_of_FOSS_licenses\n.. _BSD 2-clause license:\n https://opensource.org/licenses/BSD-2-Clause\n.. _CC BY 3.0 license:\n https://creativecommons.org/licenses/by/3.0\n\n.. # ------------------( LINKS ~ soft : py )------------------\n.. _dill:\n https://pypi.python.org/pypi/dill\n.. _imageio:\n https://imageio.github.io\n.. _Matplotlib:\n http://matplotlib.org\n.. _NumPy:\n http://www.numpy.org\n.. _PyPI:\n https://pypi.python.org\n.. _Python:\n.. _Python 3:\n https://www.python.org\n.. _pip:\n https://pip.pypa.io\n.. _SciPy:\n http://www.scipy.org\n\n.. # ------------------( LINKS ~ soft : py : conda )------------------\n.. _Anaconda:\n https://www.anaconda.com/download\n.. _Anaconda packages:\n https://anaconda.org\n.. _conda-forge:\n https://conda-forge.org\n\n.. # ------------------( LINKS ~ soft : py : package : test )------------------\n.. _Codecov:\n https://about.codecov.io\n.. _pytest:\n https://docs.pytest.org\n.. _tox:\n https://tox.readthedocs.io\n\n.. # ------------------( LINKS ~ soft : py : package : pys2 )------------------\n.. _PySide2:\n https://wiki.qt.io/PySide2\n.. _PySide2 5.6:\n https://code.qt.io/cgit/pyside/pyside.git/log/?h=5.6\n.. _PySide2 installation:\n https://wiki.qt.io/PySide2_GettingStarted\n.. _PySide2 PPA:\n https://launchpad.net/~thopiekar/+archive/ubuntu/pyside-git\n.. _Qt:\n https://www.qt.io\n.. _Qt 5.6:\n https://wiki.qt.io/Qt_5.6_Release\n",
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"license": "Copyright 2014-2025 by Alexis Pietak & Cecil Curry. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.",
"summary": "The BioElectric Tissue Simulation Engine (BETSE) is a discrete exterior calculus simulator for 2D computational multiphysics problems in the life sciences -- including (electro)diffusion, (electro)osmosis, galvanotaxis, voltage-gated ion channels, gene regulatory networks, and biochemical reaction networks.",
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