|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
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"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.io. While\nall major tools have been documented, the documentation is still a work\nin progress. A PDF copy of the documentation is also included in the\n``site-packages/psctb/docs`` subfolder of the Python prefix where\nPySCeSToolbox is installed.\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 or\nwith conda. For detailed operating system-specific instructions on\ninstalling the requirements see the documentation at\n`http://pyscestoolbox.readthedocs.io/ <http://pyscestoolbox.readthedocs.io>`__.\n\n- A Python 3.x installation (versions 3.6-3.8 recommended)\n- The full SciPy stack (see http://scipy.org/install.html)\n- PySCeS (see http://pysces.sourceforge.net/download.html)\n- Maxima (see http://maxima.sourceforge.net/download.html)\n- Jupyter Notebook (jupyter-core version in the 4.x.x series)\n\n..\n\n | **Notes:**\n | Required packages should automatically download and install when\n using the commands specified under `Installation <#installation>`__\n below.\n | Maxima is only a requirement for SymCA.\n\nInstallation\n------------\n\n **Note:** *Detailed installation instructions* are provided\n `here <https://pyscestoolbox.readthedocs.io/en/latest/installation.html>`__.\n\nThe latest release of PySCeSToolbox can be installed either on Anaconda\nor from PyPI by running the following commands in the terminal (or\nWindows equivalent).\n\nInstall on Anaconda:\n\n.. code:: bash\n\n conda install -c pysces -c sbmlteam pyscestoolbox\n\nInstall from PyPi using ``pip``:\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\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 3``\n3. Run the following three commands in the first cell:\n\n.. code:: python\n\n import pysces\n import psctb\n %matplotlib inline\n\nModel files must be placed in ``~/Pysces/psc/`` if using Linux or macOS,\nand in ``C:\\Pysces\\psc\\`` for Windows (PySCeS version < 0.9.8) or\n``C:\\Users\\<username>\\Pysces\\psc`` (PySCeS version 0.9.8+).\n\nImportant notices\n-----------------\n\nFor readers of \u201cTracing regulatory routes in metabolism using generalised supply-demand analysis\u201d published in `BMC Systems Biology <https://doi.org/10.1186/s12918-015-0236-1>`__\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nTo use the Jupyter notebook file included as \u201cAdditional file 5\u201d in the\npaper, please install the **latest version** of PySCeSToolbox specified\nunder `Installation <#installation>`__.\n\nThe two PySCeS MDL model files included as \u201cAdditional file 1\u201d and\n\u201cAdditional file 2\u201d are required to run the notebook. They should be\nrenamed to \u201cHoefnagel_moiety_ratio.psc\u201d and \u201cCurien.psc\u201d, respectively.\nFurther instructions are included within the notebook and on this page.\n\nChanges:\n~~~~~~~~\n\nBecause this project is undergoing development, future changes might\nbreak older scripts. These types of changes will be kept to a minimum\nand will be 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\u201c``jupyter nbextension enable --py --sys-prefix widgetsnbextension``\u201d\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. 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To port\nany older script simply change the old name of any method/variable to\nthe new name.\n\n**RateChar**\n\n============== ============\nOld name New Name\n============== ============\nsave save_session\nload load_session\nplot_data scan_results\nmca_data mca_results\nplot_decompose do_mca_scan\n============== ============\n\n**Thermokin**\n\n=============== ================\nOld name New Name\n=============== ================\nreactions reaction_results\nmca_data ec_results\nreaction name\\* J_reaction name\npar_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======== ============\nOld name New Name\n======== ============\nCC cc_results\nCCn\\* cc_results_n\nsave save_session\nload load_session\npar_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========= ============\nOld name New Name\n========= ============\nplot_data scan_results\nsave_data save_results\n========= ============\n\n.. |Documentation Status| image:: https://readthedocs.org/projects/pyscestoolbox/badge/?version=latest\n :target: http://pyscestoolbox.readthedocs.org/en/latest/?badge=latest\n",
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