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betse-1.3.0
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مشاهده بیشترتوضیحات
BETSE, the BioElectric Tissue Simulation Engine.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | betse-1.3.0 |
| نام | betse |
| نسخه کتابخانه | 1.3.0 |
| نگهدارنده | ['Alexis Pietak, Cecil Curry, et al.'] |
| ایمیل نگهدارنده | ['alexis.pietak@gmail.com'] |
| نویسنده | Alexis Pietak, Cecil Curry, et al. |
| ایمیل نویسنده | alexis.pietak@gmail.com |
| آدرس صفحه اصلی | https://github.com/betsee/betse |
| آدرس اینترنتی | https://pypi.org/project/betse/ |
| مجوز | 2-clause BSD |
.. # ------------------( DIRECTIVES )------------------
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.. # 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
pip3 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
نیازمندی
| مقدار | نام |
|---|---|
| >=38.2.0 | setuptools |
| >=1.22.0 | Numpy |
| >=5.3.0 | Pillow |
| >=0.12.0 | SciPy |
| >=0.2.3 | dill |
| >=3.3.4 | matplotlib |
| >=0.15.24 | ruamel.yaml |
| >=0.10.0 | beartype |
| >=1.5.2 | six |
| >=1.0.4 | distro |
| >=0.4.1 | pympler |
| >=0.29 | ptpython |
| !=1.11,>=1.8 | networkx |
| >=1.0.28 | pydot |
| >=38.2.0 | setuptools |
| >=5.4.0 | pytest |
| >=5.5 | coverage |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.8.0 | Python |
نحوه نصب
نصب پکیج whl betse-1.3.0:
pip install betse-1.3.0.whl
نصب پکیج tar.gz betse-1.3.0:
pip install betse-1.3.0.tar.gz