{ "info": { "author": "Carl Christensen", "author_email": "carldc@sun.ac.za", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Programming Language :: Python :: 2.7", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "|Documentation Status|\n\nPySCeSToolbox\n=============\n\nThis is a set of metabolic model analysis tools for PySCeS.\n\nPySCeSToolbox currently provides tools for:\n\n- Generalised supply-demand analysis.\n- Symbolic metabolic control analysis and control pattern analysis.\n- Generating model schemas from metabolic models.\n- Distinguishing between thermodynamic and kinetic contributions\n towards reaction rate.\n- Interactive plotting\n\nPySCeSToolbox was designed to be used within the Jupyter notebook, but\nmost of the core features should work in a normal Python script.\n\nDocumentation can be found at http://pyscestoolbox.readthedocs.org.\nWhile all major tools have been documented, the documentation is still a\nwork in progress.\n\nContents of README\n------------------\n\n- `Requirements <#requirements>`__\n- `Installation <#installation>`__\n- `Basic usage <#basic-usage>`__\n- `Important notices <#important-notices>`__\n- `Porting scripts to latest\n version <#porting-scripts-to-latest-version>`__\n\nRequirements\n------------\n\nAn abbreviated list of requirements is given below. Python dependencies\nwill be installed automatically when installing PySCeSToolbox via pip.\nFor detailed operating system specific instructions on installing the\nrequirements see the documentation at\n`http://pyscestoolbox.readthedocs.io/ `__,\n\n- A Python 2.7 installation\n- The full SciPy stack (see http://scipy.org/install.html)\n- PySCeS (see http://pysces.sourceforge.net/download.html or install\n using ``pip install pysces``)\n- Maxima (see http://maxima.sourceforge.net/download.html)\n- Jupyter Notebook (version in the 4.x.x series)\n\n**Notes:**\n\nRequired packages should automatically download and install when using\nthe commands specified under `Installation <#installation>`__ below.\n\nMaxima is only a requirement for SymCA.\n\nInstallation\n------------\n\nThe latest release of PySCeSToolbox can be installed from PyPi by\nrunning the following commands in the terminal (or Windows equivalent):\n\n.. code:: bash\n\n pip install pyscestoolbox\n\nTo enable widgets you may need to run the following commands:\n\n.. code:: bash\n\n jupyter nbextension enable --py --sys-prefix widgetsnbextension\n jupyter nbextension install --py --user d3networkx_psctb\n jupyter nbextension enable --py --user d3networkx_psctb\n\n\nThe latest development version can be installed from GitHub with:\n\n.. code:: bash\n\n pip install git+https://github.com/PySCeS/PySCeSToolbox.git\n\nFor the pre-2015-11-11 version:\n\n.. code:: bash\n\n pip install git+https://github.com/exe0cdc/ipython-d3networkx.git\n pip install git+https://github.com/PySCeS/PySCeSToolbox.git@f63b5ab660f103105750159885608a5f48de1551\n\nBasic usage\n-----------\n\nTo start a PySCeSToolbox session in a Jupyter notebook:\n\n1. Start up the Jupyter Notebook using the ``jupyter notebook`` command\n in the terminal\n2. Create a new notebook by clicking the ``New`` button on the top right\n of the window and selecting ``Python 2``\n3. Run the following three commands in the first cell:\n\n.. code:: python\n\n %matplotlib inline\n import pysces\n import psctb\n\nModel files must be placed in ``~/Pysces/psc/`` if using Linux or\n``C:\\Pysces\\psc\\`` for Windows.\n\nImportant notices\n-----------------\n\nFor readers of \"Tracing regulatory routes in metabolism using generalised supply-demand analysis\" published in BMC Systems Biology on 03/12/2015:\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nTo use the IPython notebook file included as \"Additional file 5\" in the\npaper, please install the **latest version** of PySCeSToolbox specified\nunder `Installation <#installation>`__.\n\nThe two PySCeS MDL model files included as \"Addition file 1\" and\n\"Addition file 2\" are required to run the notebook. They should be\nrenamed to \"Hoefnagel\\_moiety\\_ratio.psc\" and \"Curien.psc\",\nrespectively. Further instructions are included within the notebook and\non this page.\n\nFirefox users should download these files using a different browser or\nswitch to the new beta version of the BMC Systems Biology website.\n\nChanges:\n~~~~~~~~\n\nBecause this project is still in its infancy, future changes might break\nolder scripts. These types of changes will be kept to a minimum and will\nbe documented here.\n\nChanges on 2017-02-09: Full cross compatibility\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nOn 2017-02-09 Symca support via Maxima has been added to PySCeSToolbox\non Windows. A configuration file located at\n``C:\\Pysces\\psctb_config.ini`` can be used to specify the path to\n``maxima.bat``. By default, however, PySCeSToolbox should detect the\npath to ``maxima.bat`` automatically if it has been installed using the\ndefault options. This change should have no impact on any older scripts\nsave for making them platform independent.\n\nChanges on 2017-02-02: Dropped IPython Notebook 3.x.x support\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nAs of 2017-02-02 IPython Notebook 3.x.x support has been dropped in\nfavour of Jupyter 4.x.x. This should not affect the functioning of\nscripts (save for those based on versions before that of 2015-11-11).\nPySCeSToolbox will however require the Jupyter Notebook as of this date\nin order to use its interactive features. Note that ``ipywidgets`` (an\nautomatically installed requirement for the Jupyter notebook) needs you\nto run the command\n\"``jupyter nbextension enable --py --sys-prefix widgetsnbextension``\"\nbefore enabling widgets in the notebook.\n\nChanges on 2015-11-11: API changes\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nMajor changes were made on 2015-11-11 that might break scripts coded\nbefore this date. These changes are related to the naming of methods and\nfields. For scripts older than 2015-11-11 we recommend using an older\nversion of PySCeSToolbox (noted under `Installation <#installation>`__).\nManual porting of scripts is also possible with details of necessary\nchanges outlined under `Porting scripts to latest\nversion <#porting-scripts-to-latest-version>`__.\n\nPorting scripts to latest version\n---------------------------------\n\nMethod and variable names and the analysis objects they belong to that\nwere changed on 2015-11-11 are documented in the tables below. To port\nany older script simply change the old name of any method/variable to\nthe new name.\n\n**RateChar**\n\n+-------------------+-----------------+\n| Old name | New Name |\n+===================+=================+\n| save | save\\_session |\n+-------------------+-----------------+\n| load | load\\_session |\n+-------------------+-----------------+\n| plot\\_data | scan\\_results |\n+-------------------+-----------------+\n| mca\\_data | mca\\_results |\n+-------------------+-----------------+\n| plot\\_decompose | do\\_mca\\_scan |\n+-------------------+-----------------+\n\n**Thermokin**\n\n+-------------------+---------------------+\n| Old name | New Name |\n+===================+=====================+\n| reactions | reaction\\_results |\n+-------------------+---------------------+\n| mca\\_data | ec\\_results |\n+-------------------+---------------------+\n| reaction name\\* | J\\_reaction name |\n+-------------------+---------------------+\n| par\\_scan | do\\_par\\_scan |\n+-------------------+---------------------+\n\n\\*reaction name refers to the naming of a reaction as it is defined in\nthe model file.\n\n**Symca**\n\n+-------------+------------------+\n| Old name | New Name |\n+=============+==================+\n| CC | cc\\_results |\n+-------------+------------------+\n| CCn\\* | cc\\_results\\_n |\n+-------------+------------------+\n| save | save\\_session |\n+-------------+------------------+\n| load | load\\_session |\n+-------------+------------------+\n| par\\_scan | do\\_par\\_scan |\n+-------------+------------------+\n\n\\*CCn refers to any of the additional result dictionaries that are\ncreated when an internal metabolite is fixed and the ``internal_fixed``\nparamenter of ``do_symca`` is set to ``True``\n\n**Data2D**\n\n+--------------+-----------------+\n| Old name | New Name |\n+==============+=================+\n| plot\\_data | scan\\_results |\n+--------------+-----------------+\n| save\\_data | save\\_results 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