{ "info": { "author": "Nicolas Loira", "author_email": "nloira@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Environment :: Console", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU General Public License v2 (GPLv2)", "Programming Language :: Python :: 2.7", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "==============\n Pantograph\n==============\n\n-----------------------------------------------------------\n A toolbox for genome-scale metabolic model reconstruction\n-----------------------------------------------------------\n\n:Author: Nicolas Loira\n:Date: 2016-04\n\n\nBiopantograph is a collection of python modules and programs for the reconstruction, curation and validation of metabolic models. It reads and writes `SBML `_ files.\n\nInstallation\n------------\n\nThe recommended installation method is::\n\n\tpip install biopantograph\n\nPantograph 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 `_.\n\nTools\n-----\n\nThe 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 `_ and/or `OrthoMCL `_) and other optional data. Invoke ``pantograph`` as follows::\n\n\n $ pantograph -x scaffold.xml -i inparanoid.data -m orthomcl.data -s org1 -t org2 -o out.xml -l out.log\n\nWhere ```scaffold.txt``` is an existing, well-curated SBML metabolic model, used as a template for the reconstruction;\n``inparanoid.data`` is the output from Inparanoid, comparing the genes from the template and the reconstructed model;\n``orthomcl.data`` is the output from OrthoMCL (where ``org1`` is the template model id and ``org2`` is the reconstructed model id);\n``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.\n\nThe ``biopantograph`` package includes many other tools that can be useful for your reconstruction. Try them with the parameter ``--help`` to obtain usage information.\n\n===================== ===============================================================\nTool Description\n===================== ===============================================================\npantograph Create a new model, from a template model and orthology files\nptg_addbiggreactions Add reactions from a list of BiGG ids, to a model\nptg_projector Create a new model, using an existing one as template\nptg_curateSBML Add new species/reactions to a model, from a CSV\nptg_inparanoid2rel Parses Inparanoid output for ptg_projector\nptg_omcl2rel Parses OrthoMCL output for ptg_projector\n===================== ===============================================================\n\nThe modules provided can be used to develop your own applications:\n\n\n===================== =========================================================================================\nModule Description\n===================== =========================================================================================\npathtastictools Algorithms to reconstruct metabolic models from a template\nSBMLeditor High-level modifications to SBML models\nBiGG Module to handle calls to the `BiGG Web API `_\nBiGG2SBML Add elements from BiGG API to a SBML file\nSBMLutils High-level utilities\n===================== =========================================================================================\n\n\nBiopantograph 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!\n\nReference\n---------\n\nIf you use Pantograph for your own reconstructions, please cite:\n\n\tNicolas 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.\n\tDOI: 10.1142/S0219720015500067\n\nFor any question, please contact: Nicolas Loira nloira@gmail.com\n\nLicense\n-------\n\nThis project is open source and freely available under the `GLP v2 license `_.", "description_content_type": null, "docs_url": null, "download_url": "UNKNOWN", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "http://pathtastic.gforge.inria.fr", "keywords": "pantograph metabolic model reconstruction", "license": "GPLv2", "maintainer": null, "maintainer_email": null, "name": "biopantograph", "package_url": "https://pypi.org/project/biopantograph/", "platform": "UNKNOWN", "project_url": "https://pypi.org/project/biopantograph/", "project_urls": { "Download": "UNKNOWN", "Homepage": "http://pathtastic.gforge.inria.fr" }, "release_url": "https://pypi.org/project/biopantograph/0.3.2/", "requires_dist": null, "requires_python": null, "summary": "Pantograph is a toolbox for the reconstruction, curation and validation of metabolic models.", "version": "0.3.2" }, "last_serial": 2072455, "releases": { "0.3.0": [ { "comment_text": "", "digests": { "md5": "6e89728d2be406ae44ac66fca12838e9", "sha256": "fb097536a30368dcbd88bdabf2e813d1968cf566befb9cd9b2c7abac71cfbd91" }, "downloads": -1, "filename": "biopantograph-0.3.0.tar.gz", "has_sig": false, "md5_digest": "6e89728d2be406ae44ac66fca12838e9", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 35695, "upload_time": "2016-04-14T14:54:16", "url": "https://files.pythonhosted.org/packages/6b/69/24033ad944bef420dcd84ba0bbd7af4bc7cbba10139f71d3f96036144bb2/biopantograph-0.3.0.tar.gz" } ], "0.3.1": [ { "comment_text": "", "digests": { "md5": "2d470730cdee3a1ed1b52f1dc20c7436", "sha256": "29b2dcd54dee2cf7a68bea971b8fc4634225717c14a2ac16ade96bb9800243c4" }, "downloads": -1, "filename": "biopantograph-0.3.1.tar.gz", "has_sig": false, "md5_digest": "2d470730cdee3a1ed1b52f1dc20c7436", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 36293, "upload_time": "2016-04-14T15:18:12", "url": "https://files.pythonhosted.org/packages/bb/3b/16341e1d5a11efe821a2406a143524595118a09d7d11a750e4897981e656/biopantograph-0.3.1.tar.gz" } ], "0.3.2": [ { "comment_text": "", "digests": { "md5": "bc2d0ed7ec4b03050c29c2b55e477172", "sha256": "e10d37be8f70792a6ba91ae22a3125b6e05ff9648d2b0a9a9f840950d9e48b10" }, "downloads": -1, "filename": "biopantograph-0.3.2.tar.gz", "has_sig": false, "md5_digest": "bc2d0ed7ec4b03050c29c2b55e477172", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 37137, "upload_time": "2016-04-19T16:21:47", "url": "https://files.pythonhosted.org/packages/2e/81/2bb4898b1457f9c790d60fc8d74346efe726fa1a9729fbd7c3d2b55c2218/biopantograph-0.3.2.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "bc2d0ed7ec4b03050c29c2b55e477172", "sha256": "e10d37be8f70792a6ba91ae22a3125b6e05ff9648d2b0a9a9f840950d9e48b10" }, "downloads": -1, "filename": "biopantograph-0.3.2.tar.gz", "has_sig": false, "md5_digest": "bc2d0ed7ec4b03050c29c2b55e477172", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 37137, "upload_time": "2016-04-19T16:21:47", "url": "https://files.pythonhosted.org/packages/2e/81/2bb4898b1457f9c790d60fc8d74346efe726fa1a9729fbd7c3d2b55c2218/biopantograph-0.3.2.tar.gz" } ] }