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betsee-1.1.1.0
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مشاهده بیشترتوضیحات
BETSEE, the BioElectric Tissue Simulation Engine Environment.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | betsee-1.1.1.0 |
| نام | betsee |
| نسخه کتابخانه | 1.1.1.0 |
| نگهدارنده | ['Alexis Pietak, Cecil Curry, et al.'] |
| ایمیل نگهدارنده | ['leycec@gmail.com'] |
| نویسنده | Alexis Pietak, Cecil Curry, et al. |
| ایمیل نویسنده | leycec@gmail.com |
| آدرس صفحه اصلی | https://gitlab.com/betse/betsee |
| آدرس اینترنتی | https://pypi.org/project/betsee/ |
| مجوز | 2-clause BSD |
.. # ------------------( DIRECTIVES )------------------
.. # Fallback language applied to all code blocks failing to specify an
.. # explicit language. Since the majority of all code blocks in this document
.. # are Bash one-liners intended to be run interactively, this is "console".
.. # For a list of all supported languages, see also:
.. # http://build-me-the-docs-please.readthedocs.org/en/latest/Using_Sphinx/ShowingCodeExamplesInSphinx.html#pygments-lexers
.. # FIXME: Sadly, this appears to be unsupported by some ReST parsers and hence
.. # is disabled until more widely supported. *collective shrug*
.. # highlight:: console
.. # ------------------( SYNOPSIS )------------------
======
BETSEE
======
**BETSEE** (**B**\ io\ **E**\ lectric **T**\ issue **S**\ imulation **E**\
ngine **E**\ nvironment) is the open-source cross-platform graphical user
interface (GUI) for BETSE_, a `finite volume`_ simulator for 2D computational
multiphysics problems in the life sciences – including electrodiffusion_,
electro-osmosis_, galvanotaxis_, `voltage-gated ion channels`_, `gene
regulatory networks`_, and `biochemical reaction networks`_ (e.g., metabolism).
Like BETSE_, BETSEE is `portably implemented <codebase_>`__ in pure `Python 3
<Python_>`__, `continuously stress-tested <testing_>`__ with GitLab-CI_ **×**
Appveyor_ **+** py.test_, and `permissively distributed <License_>`__ under the
`BSD 2-clause license`_.
.. # ------------------( TABLE OF CONTENTS )------------------
.. # Blank line. By default, Docutils appears to only separate the subsequent
.. # table of contents heading from the prior paragraph by less than a single
.. # blank line, hampering this table's readability and aesthetic comeliness.
|
.. # Table of contents, excluding the above document heading. While the
.. # official reStructuredText documentation suggests that a language-specific
.. # heading will automatically prepend this table, this does *NOT* appear to
.. # be the case. Instead, this heading must be explicitly declared.
.. contents:: **Contents**
:local:
.. # ------------------( DESCRIPTION )------------------
Installation
============
BETSEE is universally installable with either:
- [\ *Recommended*\ ] pip_, the standard Python package manager:
.. code-block:: console
pip3 install betsee
- Anaconda_, a third-party Python package manager:
.. code-block:: console
conda config --add channels conda-forge
conda install betsee
See our `installation instructions <BETSE install_>`__ for details. [#install_betse]_
.. [#install_betse]
Globally replace all instances of the substring ``betse`` with ``betsee``
(e.g., ``pip3 install betsee`` rather than ``pip3 install betse``) in these
instructions, which technically refer to BETSE rather than BETSEE.
License
=======
BETSEE is open-source software `released <LICENSE>`__ under the permissive `BSD
2-clause license`_. BETSEE contains third-party assets also released under
`BSD-compatible licenses <license compatibility_>`__, including:
* All `Entypo+ icons`_ `distributed with BETSEE <BETSEE Entypo+ icons_>`__,
`kindly released <Entypo+ license_>`__ under the permissive `CC BY-SA 4.0
license`_ by `Daniel Bruce`_.
* All `Noun Project icons`_ `distributed with BETSEE <BETSEE Noun Project
icons_>`__, `kindly released <Noun Project license_>`__ under the permissive
`CC BY 3.0 license`_ by various authors, including:
* `Maxim Kulikov`_, author of the `salubrious bovine <Cows collection_>`__
prominently displayed on this `project page <project_>`__.
* All `Open Iconic icons`_ `distributed with BETSEE <BETSEE Open Iconic
icons_>`__, `kindly released <Open Iconic license_>`__ under the permissive
`MIT license`_.
Citation
=========
BETSE_ is formally described in our `introductory paper <2016 article_>`__.
Third-party papers, theses, and other texts leveraging BETSEE (and hence
BETSE_) should ideally cite the following:
`Alexis Pietak`_ and `Michael Levin`_, 2016. |2016 article name|_
|2016 article supplement|_ [#supplement]_ |2016 journal name|_ *4*\ (55).
:sup:`https://doi.org/10.3389/fbioe.2016.00055`
See also `this list of BETSE-centric papers <BETSE citation_>`__ for
additional material.
.. [#supplement]
This article's supplement extends the cursory theory presented by this
article with a rigorous treatment of the mathematics, formalisms, and
abstractions required to fully reproduce this work. If theoretical questions
remain after completing the main article, please consult this supplement.
Authors
=======
BETSEE comes courtesy a dedicated community of `authors <author list_>`__ and
contributors_ – without whom this project would be computationally
impoverished, biologically misaligned, and simply unusable.
**Thanks, all.**
Funding
=======
BETSEE is currently independently financed as a volunteer open-source project.
Prior grant funding sources include (in chronological order):
#. For the three year period spanning 2017—2019, BETSEE 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`_ .
.. # ------------------( LINKS ~ betse )------------------
.. _BETSE:
https://gitlab.com/betse/betse
.. _BETSE citation:
https://gitlab.com/betse/betse#citation
.. _BETSE install:
https://gitlab.com/betse/betse/blob/master/doc/rst/INSTALL.rst
.. _BETSE live:
https://gitlab.com/betse/betse#advanced
.. # ------------------( LINKS ~ betsee )------------------
.. _author list:
doc/rst/AUTHORS.rst
.. _codebase:
https://gitlab.com/betse/betsee/tree/master
.. _conda package:
https://anaconda.org/conda-forge/betsee
.. _contributors:
https://gitlab.com/betse/betsee/graphs/master
.. _dependencies:
doc/md/INSTALL.md
.. _project:
https://gitlab.com/betse/betsee
.. _PyPI package:
https://pypi.org/project/betsee
.. _testing:
https://gitlab.com/betse/betsee/pipelines
.. _tarballs:
https://gitlab.com/betse/betsee/tags
.. _Ubuntu 16.04 installer:
https://gitlab.com/betse/betsee/blob/master/bin/install/linux/betsee_ubuntu_16_04.bash
.. # ------------------( LINKS ~ academia )------------------
.. _Alexis Pietak:
.. _Pietak, Alexis:
https://www.researchgate.net/profile/Alexis_Pietak
.. _Michael Levin:
.. _Levin, Michael:
https://ase.tufts.edu/biology/labs/levin
.. _Paul Allen Discovery Center:
http://www.alleninstitute.org/what-we-do/frontiers-group/discovery-centers/allen-discovery-center-tufts-university
.. _Paul Allen Discovery Center award:
https://www.alleninstitute.org/what-we-do/frontiers-group/news-press/press-resources/press-releases/paul-g-allen-frontiers-group-announces-allen-discovery-center-tufts-university
.. _Paul G. Allen Frontiers Group:
https://www.alleninstitute.org/what-we-do/frontiers-group
.. _Tufts University:
https://www.tufts.edu
.. # ------------------( LINKS ~ paper : 2016 )------------------
.. _2016 article:
http://journal.frontiersin.org/article/10.3389/fbioe.2016.00055/abstract
.. |2016 article name| replace::
**Exploring instructive physiological signaling with the bioelectric tissue
simulation engine (BETSE).**
.. _2016 article name:
http://journal.frontiersin.org/article/10.3389/fbioe.2016.00055/abstract
.. |2016 article supplement| replace::
**(**\ Supplement\ **).**
.. _2016 article supplement:
https://www.frontiersin.org/articles/file/downloadfile/203679_supplementary-materials_datasheets_1_pdf/octet-stream/Data%20Sheet%201.PDF/1/203679
.. |2016 journal name| replace::
*Frontiers in Bioengineering and Biotechnology,*
.. _2016 journal name:
http://journal.frontiersin.org/journal/bioengineering-and-biotechnology
.. # ------------------( LINKS ~ science )------------------
.. _biochemical reaction networks:
http://www.nature.com/subjects/biochemical-reaction-networks
.. _electrodiffusion:
https://en.wikipedia.org/wiki/Nernst%E2%80%93Planck_equation
.. _electro-osmosis:
https://en.wikipedia.org/wiki/Electro-osmosis
.. _finite volume:
https://en.wikipedia.org/wiki/Finite_volume_method
.. _galvanotaxis:
https://en.wiktionary.org/wiki/galvanotaxis
.. _gene regulatory networks:
https://en.wikipedia.org/wiki/Gene_regulatory_network
.. _voltage-gated ion channels:
https://en.wikipedia.org/wiki/Voltage-gated_ion_channel
.. # ------------------( LINKS ~ os : linux )------------------
.. _APT:
https://en.wikipedia.org/wiki/Advanced_Packaging_Tool
.. _Arch Linux:
https://www.archlinux.org
.. _CentOS:
https://www.centos.org
.. _Gentoo Linux:
https://gentoo.org
.. _Ubuntu:
.. _Ubuntu Linux:
https://www.ubuntu.com
.. _Ubuntu Linux 16.04 (Xenial Xerus):
http://releases.ubuntu.com/16.04
.. # ------------------( LINKS ~ os : windows )------------------
.. _WSL:
https://msdn.microsoft.com/en-us/commandline/wsl/install-win10
.. # ------------------( LINKS ~ soft )------------------
.. _Appveyor:
https://ci.appveyor.com/project/betse/betse/branch/master
.. _Bash on Ubuntu on Windows:
http://www.windowscentral.com/how-install-bash-shell-command-line-windows-10
.. _FFmpeg:
https://ffmpeg.org
.. _Git:
https://git-scm.com/downloads
.. _GitLab-CI:
https://about.gitlab.com/gitlab-ci
.. _Graphviz:
http://www.graphviz.org
.. _Homebrew:
http://brew.sh
.. _Libav:
https://libav.org
.. _macOS:
https://en.wikipedia.org/wiki/Macintosh_operating_systems
.. _MacPorts:
https://www.macports.org
.. _MEncoder:
https://en.wikipedia.org/wiki/MEncoder
.. _OpenBLAS:
https://www.openblas.net
.. _POSIX:
https://en.wikipedia.org/wiki/POSIX
.. _PPA:
https://launchpad.net/ubuntu/+ppas
.. _VirtualBox:
https://www.virtualbox.org
.. _YAML:
http://yaml.org
.. # ------------------( LINKS ~ soft : icon )------------------
.. _BETSEE Entypo+ icons:
betsee/data/qrc/icon/entypo+
.. _BETSEE Noun Project icons:
betsee/data/qrc/icon/nounproject
.. _BETSEE Open Iconic icons:
betsee/data/qrc/icon/open_iconic
.. _Cows collection:
https://thenounproject.com/maxim221/collection/cows
.. _Daniel Bruce:
http://www.danielbruce.se
.. _Entypo+ icons:
http://entypo.com
.. _Maxim Kulikov:
https://thenounproject.com/maxim221
.. _Noun Project:
.. _Noun Project icons:
https://thenounproject.com
.. _Noun Project license:
https://thenounproject.com/legal
.. _Open Iconic icons:
https://github.com/iconic/open-iconic
.. # ------------------( LINKS ~ 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
.. _CC BY-SA 4.0 license:
https://creativecommons.org/licenses/by-sa/4.0
.. _Entypo+ license:
licenses/entypo+
.. _MIT license:
https://opensource.org/licenses/MIT
.. _Open Iconic license:
licenses/open_iconic
.. # ------------------( 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
.. _py.test:
http://pytest.org
.. _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
.. _Miniconda:
https://conda.io/miniconda.html
.. # ------------------( LINKS ~ soft : py : pyside2 )------------------
.. _PySide2:
https://wiki.qt.io/PySide2
.. _PySide2 5.9:
http://code.qt.io/cgit/pyside/pyside-setup.git/log/?h=5.9
.. _PySide2 feedstock:
https://github.com/conda-forge/pyside2-feedstock
.. _PySide2 installation:
https://wiki.qt.io/PySide2_GettingStarted
.. _PySide2 PPA:
https://launchpad.net/~thopiekar/+archive/ubuntu/pyside-git
.. _PySide2 wheels:
https://github.com/fredrikaverpil/pyside2-wheels/blob/master/QUICKSTART.md
.. _Qt:
https://www.qt.io
.. _Qt 5.9:
https://wiki.qt.io/Qt_5.9_Release
نیازمندی
| مقدار | نام |
|---|---|
| >=5.12.3 | PySide2 |
| ==1.1.1 | betse |
| >=38.2.0 | setuptools |
| >=3.7.0) | pytest |
| >=3.2.0) | pytest-qt |
| >=1.2.0) | pytest-xvfb |
| >=38.2.0) | setuptools |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.5.0 | Python |
نحوه نصب
نصب پکیج whl betsee-1.1.1.0:
pip install betsee-1.1.1.0.whl
نصب پکیج tar.gz betsee-1.1.1.0:
pip install betsee-1.1.1.0.tar.gz