Metadata-Version: 1.1
Name: PyscesToolbox
Version: 1.0.0
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/1.0.0.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 or
        with conda. 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)
        -  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 either on Anaconda
        or from PyPI by running the following commands in the terminal (or
        Windows equivalent).
        
        Install on Anaconda:
        
        .. code:: bash
        
           conda install -c pysces -c sbmlteam pyscestoolbox
        
        Install from PyPi using ``pip``:
        
        .. 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 “Additional file 1” and
        “Additional 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
