Metadata-Version: 1.1
Name: biopantograph
Version: 0.3.2
Summary: Pantograph is a toolbox for the reconstruction, curation and validation of metabolic models.
Home-page: http://pathtastic.gforge.inria.fr
Author: Nicolas Loira
Author-email: nloira@gmail.com
License: GPLv2
Description: 
        
        ==============
         Pantograph
        ==============
        
        -----------------------------------------------------------
         A toolbox for genome-scale metabolic model reconstruction
        -----------------------------------------------------------
        
        :Author: Nicolas Loira
        :Date: 2016-04
        
        
        Biopantograph is a collection of python modules and programs for the reconstruction, curation and validation of metabolic models. It reads and writes `SBML <http://sbml.org/Main_Page>`_ files.
        
        Installation
        ------------
        
        The recommended installation method is::
        
        	pip install biopantograph
        
        Pantograph requires ``libsbml``, but ``pip`` will take care of that requirement. If you don't have permissions to install at the system level, try: ``pip install biopantograph --user``. You can also clone and contribute from the `BitBucket repository <https://bitbucket.org/nloira/pantograph>`_.
        
        Tools
        -----
        
        The basic script you need to know is ``pantograph``, which will help you to reconstruct a metabolic model for your target species. ``pantograph`` takes as input an existing SBML model as a template, orthology data between your template and your target genes (from `Inparanoid  <http://inparanoid.sbc.su.se/cgi-bin/index.cgi>`_ and/or `OrthoMCL <http://www.orthomcl.org>`_) and other optional data. Invoke ``pantograph`` as follows::
        
        
            $ pantograph -x scaffold.xml -i inparanoid.data -m orthomcl.data -s org1 -t org2 -o out.xml -l out.log
        
        Where ```scaffold.txt``` is an existing, well-curated SBML metabolic model, used as a template for the reconstruction;
        ``inparanoid.data`` is the output from Inparanoid, comparing the genes from the template and the reconstructed model;
        ``orthomcl.data`` is the output from OrthoMCL (where ``org1`` is the template model id and ``org2`` is the reconstructed model id);
        ``out.xml`` is the SBML reconstructed model and ``out.log`` is the reconstruction log. You can reconstruct a model using any of the two orthology methods (Inparanoid or OrthoMCL), although better results are obtained using both.
        
        The ``biopantograph`` package includes many other tools that can be useful for your reconstruction. Try them with the parameter ``--help`` to obtain usage information.
        
        ===================== ===============================================================
        Tool                  Description
        ===================== ===============================================================
        pantograph            Create a new model, from a template model and orthology files
        ptg_addbiggreactions  Add reactions from a list of BiGG ids, to a model
        ptg_projector         Create a new model, using an existing one as template
        ptg_curateSBML        Add new species/reactions to a model, from a CSV
        ptg_inparanoid2rel    Parses Inparanoid output for ptg_projector
        ptg_omcl2rel          Parses OrthoMCL output for ptg_projector
        ===================== ===============================================================
        
        The modules provided can be used to develop your own applications:
        
        
        ===================== =========================================================================================
        Module                Description
        ===================== =========================================================================================
        pathtastictools       Algorithms to reconstruct metabolic models from a template
        SBMLeditor            High-level modifications to SBML models
        BiGG                  Module to handle calls to the `BiGG Web API <http://bigg.ucsd.edu/data_access>`_
        BiGG2SBML             Add elements from BiGG API to a SBML file
        SBMLutils             High-level utilities
        ===================== =========================================================================================
        
        
        Biopantograph has been tested under Linux and OS X. For more information, please visit the official Pantograph website: http://pathtastic.gforge.inria.fr. More documentation coming soon!
        
        Reference
        ---------
        
        If you use Pantograph for your own reconstructions, please cite:
        
        	Nicolas Loira, Anna Zhukova and David J Sherman. *Pantograph: A template-based method for genome-scale metabolic model reconstruction.* J Bioinform Comput Biol, 13(2): 1550006, 2015.
        	DOI: 10.1142/S0219720015500067
        
        For any question, please contact: Nicolas Loira nloira@gmail.com
        
        License
        -------
        
        This project is open source and freely available under the `GLP v2 license <http://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html>`_.
        
        
Keywords: pantograph metabolic model reconstruction
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
