Metadata-Version: 2.1
Name: biomodels-qc
Version: 0.0.1
Summary: Tools for quality controlling the BioModels database
Home-page: https://github.com/biosimulations/biomodels-qc
Download-URL: https://github.com/biosimulations/biomodels-qc
Author: BioSimulations Team
Author-email: info@biosimulations.org
License: MIT
Keywords: systems biology modeling simulation
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
License-File: LICENSE
Requires-Dist: biosimulators-utils[containers,sbml] (>=0.1.171)
Requires-Dist: cement
Requires-Dist: kisao
Requires-Dist: lxml
Requires-Dist: nbformat
Requires-Dist: owlready2
Requires-Dist: pypdf2
Requires-Dist: python-copasi
Requires-Dist: python-dateutil
Requires-Dist: python-libsbml
Requires-Dist: scipy
Requires-Dist: termcolor
Requires-Dist: xmldiff
Provides-Extra: all
Requires-Dist: capturer ; extra == 'all'
Requires-Dist: pytest ; extra == 'all'
Requires-Dist: pytest-cov ; extra == 'all'
Provides-Extra: docs
Provides-Extra: tests
Requires-Dist: capturer ; extra == 'tests'
Requires-Dist: pytest ; extra == 'tests'
Requires-Dist: pytest-cov ; extra == 'tests'

|Latest release| |PyPI| |CI status| |Test coverage|

BioModels-QC
============

Command-line application for quality controlling entries in the
`BioModels database <https://www.ebi.ac.uk/biomodels/>`__ and converting
the primary files for entries in the database into additional formats
such as BioPAX, MATLAB/Octave, and XPP.

The application can be installed locally or executed as a Docker image.

This application is intended to be used in conjuction with the best
practices recommended
`here <best-practices-for-curating-biomodels.md>`__.

Local installation
------------------

Requirements
~~~~~~~~~~~~

-  `Python <https://python.org>`__ 3.9.0+
-  `pip <https://pip.pypa.io/>`__ >= 19.3
-  `Systems Biology Format
   Converter <http://sbfc.sourceforge.net/mediawiki/index.php/Main_Page>`__

   -  `Java <https://www.java.com/>`__

-  `Octave <https://www.gnu.org/software/octave/>`__

   -  `Mac OS
      installer <https://www.gnu.org/software/octave/download>`__
   -  Ubuntu: ``apt-get install octave``
   -  `Windows
      installer <https://www.gnu.org/software/octave/download>`__

-  `Scilab <https://www.scilab.org/>`__

   -  `Mac OS installer <https://www.scilab.org/download/>`__
   -  Ubuntu: ``apt-get install scilab``
   -  `Windows installer <https://www.scilab.org/download/>`__

-  `SVGLint <https://www.npmjs.com/package/svglint>`__

   -  `Node.js <https://nodejs.org/en/>`__

      -  `Mac OS installer <https://nodejs.org/en/download/>`__
      -  `Ubuntu
         instructions <https://github.com/nodesource/distributions/blob/master/README.md>`__
      -  `Windows installer <https://nodejs.org/en/download/>`__

-  `XPP <http://www.math.pitt.edu/~bard/xpp/xpp.html>`__

   -  `Mac OS
      instructions <http://www.math.pitt.edu/~bard/xpp/installonmac.html>`__
   -  Ubuntu: ``apt-get install xppaut``
   -  `Windows
      instructions <http://www.math.pitt.edu/~bard/xpp/installonwindows.html>`__

After installing the packages above, the following must be added to your
system path:

-  ``sbfConverter.sh`` (Linux/Mac OS) or ``sbfConverter.bat`` (Windows)
-  ``svglint``
-  ``xppaut``

Installation
~~~~~~~~~~~~

Run the following command to install the package.

::

   pip install biomodels-qc

Docker image
------------

Run the following command to pull the Docker image

::

   docker pull ghcr.io/biosimulations/biomodels_qc

Tutorial
--------

Convert the files for an entry to additional formats
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Run the following command to convert the files for an entry to
additional formats such as BioPAX, MATLAB/Octave, and XPP.

::

   ENTRY_DIR=/path/to/directory-for-entry
   biomodels-qc convert "$ENTRY_DIR"

Validate an entry
~~~~~~~~~~~~~~~~~

Run the following command to validate an entry of the BioModels
database:

::

   ENTRY_DIR=/path/to/directory-for-entry
   biomodels-qc validate "$ENTRY_DIR"

Using the Docker image
~~~~~~~~~~~~~~~~~~~~~~

Run the following commands to use the BioModels-QC Docker image to
execute the same conversion and validation operations.

.. _convert-the-files-for-an-entry-to-additional-formats-1:

Convert the files for an entry to additional formats
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

::

   ENTRY_DIR=/path/to/directory-for-entry\
   docker run \
       --mount type=bind,source="$ENTRY_DIR",target=/biomodels-entry \
       --interactive \
       --tty \
       --rm \
       ghcr.io/biosimulations/biomodels_qc \
           convert \
               /biomodels-entry

.. _validate-an-entry-1:

Validate an entry
^^^^^^^^^^^^^^^^^

::

   ENTRY_DIR=/path/to/directory-for-entry
   CONTAINER_TEMP_DIR=$(mktemp --directory)
   docker run \
       --mount type=bind,source="$ENTRY_DIR",target=/biomodels-entry \
       --volume /var/run/docker.sock:/var/run/docker.sock \
       --mount type=bind,source="$CONTAINER_TEMP_DIR",target=/tmp \
       --env TEMP_DIR_HOST_PATH=$CONTAINER_TEMP_DIR \
       --interactive \
       --tty \
       --rm \
       ghcr.io/biosimulations/biomodels_qc \
           validate \
               /biomodels-entry

Documentation
-------------

Documentation for the command-line program is available inline.

Run the following command to obtain the help.

::

   biomodels-qc --help

.. _using-the-docker-image-1:

Using the Docker image
~~~~~~~~~~~~~~~~~~~~~~

Run the following command to use the BioModels-QC Docker image to obtain
the help.

::

   docker run \
       --interactive \
       --tty \
       --rm \
       ghcr.io/biosimulations/biomodels_qc \
           --help

API documentation
-----------------

API documentation is available
`here <https://biosimulations.github.io/biomodels-qc/>`__.

License
-------

This package is released under the `MIT license <LICENSE>`__.

Development team
----------------

This package was developed by the `Karr Lab <https://karrlab.org>`__ at
the Icahn School of Medicine at Mount Sinai and the `Center for
Reproducible Biomedical Modeling <http://reproduciblebiomodels.org>`__.

Contributing to BioModels-QC
----------------------------

We enthusiastically welcome contributions! Please see the `guide to
contributing <CONTRIBUTING.md>`__ and the `developer's code of
conduct <CODE_OF_CONDUCT.md>`__.

Acknowledgements
----------------

This work was supported by National Institutes of Health award
P41EB023912.

Questions and comments
----------------------

Please contact the `BioSimulations
Team <mailto:info@biosimulations.org>`__ with any questions or comments.

.. |Latest release| image:: https://img.shields.io/github/v/release/biosimulations/biomodels-qc
   :target: https://github.com/biosimulations/biomodels-qc/releases
.. |PyPI| image:: https://img.shields.io/pypi/v/biomodels-qc
   :target: https://pypi.org/project/biomodels-qc/
.. |CI status| image:: https://github.com/biosimulations/biomodels-qc/workflows/Continuous%20integration/badge.svg
   :target: https://github.com/biosimulations/biomodels-qc/actions?query=workflow%3A%22Continuous+integration%22
.. |Test coverage| image:: https://codecov.io/gh/biosimulations/biomodels-qc/branch/dev/graph/badge.svg
   :target: https://codecov.io/gh/biosimulations/biomodels-qc


