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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.. # ------------------( SYNOPSIS )------------------
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_.
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.. # ------------------( DESCRIPTION )------------------
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_>__.
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.
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
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
BETSE also provides external documentation optimized for offline reading – complete with explanatory examples, sample plots, and ample screenshots:
BETSE 1.0 documentation_. (\ PDF format; 75 pages.\ )BETSE 0.4 documentation_. (\ PDF format; 72 pages.\ )BETSE 0.3 documentation_. (\ PDF format; 77 pages.\ )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:
BETSE Tutorial Simulation Packages <tutorial user_>__. (\ YAML
format.\ )BETSE Developer's Tutorial <tutorial dev_>__. (\ Jupyter
Notebook format.\ )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:
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:
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:
Simulations may enable arbitrary combinations of the principal ions implicated in bioelectrical signaling – including:
+).+).-).2+).+).Anionic proteins_ (P\ :sup:-).-\ :sub:3).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:
Custom ion channels parametrized by user-selected constants may be trivially defined in the same manner (e.g., via a YAML_\ -formatted configuration file).
For fine-grained control over cell dynamics, notable ion pumps and exchangers may also be selectively enabled – including:
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).
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.
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.
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_>__.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.
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]_
{dot} pietak{dot} comTo 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:
{dot} substring with the . charecter.@ character.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.
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_.
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_.
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
FAQs
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.
We found that betse demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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