Metadata-Version: 1.1
Name: PyscesToolbox
Version: 0.9.0
Summary: A set of metabolic model analysis tools for PySCeS.
Home-page: https://github.com/PySCeS/PyscesToolbox
Author: Carl Christensen and Johann Rohwer
Author-email: exe0cdc@gmail.com, j.m.rohwer@gmail.com
License: BSD-3-Clause
Download-URL: http://github.com/PySCeS/PyscesToolbox/archive/0.9.0.tar.gz
Description: |Documentation Status|
        
        PySCeSToolbox
        =============
        
        This is a set of metabolic model analysis tools for PySCeS.
        
        PySCeSToolbox currently provides tools for:
        
        -  Generalised supply-demand analysis.
        -  Symbolic metabolic control analysis and control pattern analysis.
        -  Generating model schemas from metabolic models.
        -  Distinguishing between thermodynamic and kinetic contributions
           towards reaction rate.
        -  Interactive plotting
        
        PySCeSToolbox was designed to be used within the Jupyter notebook, but
        most of the core features should work in a normal Python script.
        
        Documentation can be found at http://pyscestoolbox.readthedocs.io. While
        all major tools have been documented, the documentation is still a work
        in progress. A PDF copy of the documentation is also included in the
        ``site-packages/psctb/docs`` subfolder of the Python prefix where
        PySCeSToolbox is installed.
        
        Contents of README
        ------------------
        
        -  `Requirements <#requirements>`__
        -  `Installation <#installation>`__
        -  `Basic usage <#basic-usage>`__
        -  `Important notices <#important-notices>`__
        -  `Porting scripts to latest
           version <#porting-scripts-to-latest-version>`__
        
        Requirements
        ------------
        
        An abbreviated list of requirements is given below. Python dependencies
        will be installed automatically when installing PySCeSToolbox via pip.
        For detailed operating system specific instructions on installing the
        requirements see the documentation at
        `http://pyscestoolbox.readthedocs.io/ <http://pyscestoolbox.readthedocs.io>`__.
        
        -  A Python 3.x installation (versions 3.6-3.8 recommended)
        -  The full SciPy stack (see http://scipy.org/install.html)
        -  PySCeS (see http://pysces.sourceforge.net/download.html or install
           using ``pip install pysces``)
        -  Maxima (see http://maxima.sourceforge.net/download.html)
        -  Jupyter Notebook (jupyter-core version in the 4.x.x series)
        
        **Notes:**
        
        Required packages should automatically download and install when using
        the commands specified under `Installation <#installation>`__ below.
        
        Maxima is only a requirement for SymCA.
        
        Installation
        ------------
        
            **Note:** Detailed installation instructions are provided
            `here <https://pyscestoolbox.readthedocs.io/en/latest/installation.html>`__.
        
        The latest release of PySCeSToolbox can be installed from PyPi by
        running the following commands in the terminal (or Windows equivalent):
        
        .. code:: bash
        
            pip install pyscestoolbox
        
        To enable widgets you may need to run the following commands:
        
        .. code:: bash
        
            jupyter nbextension enable --py --sys-prefix widgetsnbextension
            jupyter nbextension install --py --user d3networkx_psctb
            jupyter nbextension enable --py --user d3networkx_psctb
        
        The latest development version can be installed from GitHub with:
        
        .. code:: bash
        
            pip install git+https://github.com/PySCeS/PySCeSToolbox.git
        
        For the pre-2015-11-11 version:
        
        .. code:: bash
        
            pip install git+https://github.com/exe0cdc/ipython-d3networkx.git
            pip install git+https://github.com/PySCeS/PySCeSToolbox.git@f63b5ab660f103105750159885608a5f48de1551
        
        Basic usage
        -----------
        
        To start a PySCeSToolbox session in a Jupyter notebook:
        
        1. Start up the Jupyter Notebook using the ``jupyter notebook`` command
           in the terminal
        2. Create a new notebook by clicking the ``New`` button on the top right
           of the window and selecting ``Python 3``
        3. Run the following three commands in the first cell:
        
        .. code:: python
        
            import pysces
            import psctb
            %matplotlib inline
        
        Model files must be placed in ``~/Pysces/psc/`` if using Linux or macOS,
        and in ``C:\Pysces\psc\`` for Windows (PySCeS version < 0.9.8) or
        ``C:\Users\<username>\Pysces\psc`` (PySCeS version 0.9.8+).
        
        Important notices
        -----------------
        
        For readers of "Tracing regulatory routes in metabolism using generalised supply-demand analysis" published in `BMC Systems Biology <https://doi.org/10.1186/s12918-015-0236-1>`__
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        To use the Jupyter notebook file included as "Additional file 5" in the
        paper, please install the **latest version** of PySCeSToolbox specified
        under `Installation <#installation>`__.
        
        The two PySCeS MDL model files included as "Addition file 1" and
        "Addition file 2" are required to run the notebook. They should be
        renamed to "Hoefnagel\_moiety\_ratio.psc" and "Curien.psc",
        respectively. Further instructions are included within the notebook and
        on this page.
        
        Changes:
        ~~~~~~~~
        
        Because this project is undergoing development, future changes might
        break older scripts. These types of changes will be kept to a minimum
        and will be documented here.
        
        Changes on 2017-02-09: Full cross compatibility
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        On 2017-02-09 Symca support via Maxima has been added to PySCeSToolbox
        on Windows. A configuration file located at
        ``C:\Pysces\psctb_config.ini`` can be used to specify the path to
        ``maxima.bat``. By default, however, PySCeSToolbox should detect the
        path to ``maxima.bat`` automatically if it has been installed using the
        default options. This change should have no impact on any older scripts
        save for making them platform independent.
        
        Changes on 2017-02-02: Dropped IPython Notebook 3.x.x support
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        As of 2017-02-02 IPython Notebook 3.x.x support has been dropped in
        favour of Jupyter 4.x.x. This should not affect the functioning of
        scripts (save for those based on versions before that of 2015-11-11).
        PySCeSToolbox will however require the Jupyter Notebook as of this date
        in order to use its interactive features. Note that ``ipywidgets`` (an
        automatically installed requirement for the Jupyter notebook) needs you
        to run the command
        "``jupyter nbextension enable --py  --sys-prefix widgetsnbextension``"
        before enabling widgets in the notebook.
        
        Changes on 2015-11-11: API changes
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        Major changes were made on 2015-11-11 that might break scripts coded
        before this date. These changes are related to the naming of methods and
        fields. For scripts older than 2015-11-11 we recommend using an older
        version of PySCeSToolbox (noted under `Installation <#installation>`__).
        Manual porting of scripts is also possible with details of necessary
        changes outlined under `Porting scripts to latest
        version <#porting-scripts-to-latest-version>`__.
        
        Porting scripts to latest version
        ---------------------------------
        
        Method and variable names and the analysis objects they belong to that
        were changed on 2015-11-11 are documented in the tables below. To port
        any older script simply change the old name of any method/variable to
        the new name.
        
        **RateChar**
        
        +-------------------+-----------------+
        | Old name          | New Name        |
        +===================+=================+
        | save              | save\_session   |
        +-------------------+-----------------+
        | load              | load\_session   |
        +-------------------+-----------------+
        | plot\_data        | scan\_results   |
        +-------------------+-----------------+
        | mca\_data         | mca\_results    |
        +-------------------+-----------------+
        | plot\_decompose   | do\_mca\_scan   |
        +-------------------+-----------------+
        
        **Thermokin**
        
        +-------------------+---------------------+
        | Old name          | New Name            |
        +===================+=====================+
        | reactions         | reaction\_results   |
        +-------------------+---------------------+
        | mca\_data         | ec\_results         |
        +-------------------+---------------------+
        | reaction name\*   | J\_reaction name    |
        +-------------------+---------------------+
        | par\_scan         | do\_par\_scan       |
        +-------------------+---------------------+
        
        \*reaction name refers to the naming of a reaction as it is defined in
        the model file.
        
        **Symca**
        
        +-------------+------------------+
        | Old name    | New Name         |
        +=============+==================+
        | CC          | cc\_results      |
        +-------------+------------------+
        | CCn\*       | cc\_results\_n   |
        +-------------+------------------+
        | save        | save\_session    |
        +-------------+------------------+
        | load        | load\_session    |
        +-------------+------------------+
        | par\_scan   | do\_par\_scan    |
        +-------------+------------------+
        
        \*CCn refers to any of the additional result dictionaries that are
        created when an internal metabolite is fixed and the ``internal_fixed``
        paramenter of ``do_symca`` is set to ``True``
        
        **Data2D**
        
        +--------------+-----------------+
        | Old name     | New Name        |
        +==============+=================+
        | plot\_data   | scan\_results   |
        +--------------+-----------------+
        | save\_data   | save\_results   |
        +--------------+-----------------+
        
        .. |Documentation Status| image:: https://readthedocs.org/projects/pyscestoolbox/badge/?version=latest
           :target: http://pyscestoolbox.readthedocs.org/en/latest/?badge=latest
        
Keywords: metabolism,metabolic control analysis,modelling
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3
