{ "info": { "author": "Michael Mundy, Helena Mendes-Soares, Nicholas Chia", "author_email": "mundy.michael@mayo.edu", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Environment :: Console", "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Operating System :: OS Independent", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Topic :: Scientific/Engineering", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "CobraBabel: COBRA Model Translator\n==================================\n\nMetabolic models are available from many sources and different source systems use different\nID namespaces. That makes combining and comparing models from different sources\ndifficult. CobraBabel supports the following source systems:\n\n1. `Virtual Metabolic Human `_ (VMH)\n2. `Biochemical, Genetic and Genomic knowledge base `_ (BiGG)\n3. `MetaNetX `_\n4. `Kyoto Encyclopedia of Genes and Genomes `_ (KEGG)\n\nFeatures include:\n\n* Create a universal model from VMH, BiGG, MetaNetX\n* Get a list of available models from BiGG\n* Create an organism model from VMH, BiGG\n* Get a specific reaction or metabolite from BiGG, KEGG\n* Get a specific enzyme, DNA sequence, or amino acid sequence from KEGG\n\nInstallation\n------------\n\nUse pip to install CobraBabel from\n`PyPI `_ (we recommend doing this\ninside a `virtual environment\n`_)::\n\n pip install cobrababel\n\nSource systems\n--------------\n\nCobraBabel uses the data access methods provided by the source systems. The current\nversion of the source system supported by CobraBabel is shown below. If a source\nsystem changes its interface, it is possible for CobraBabel to return an error or\nincorrect data. Additional details on the source systems are in the notes below.\n\nCobraBabel uses web services provided by other organizations which can be offline,\nthe interface can change, or the URL can change. CobraBabel uses these default URLs:\n\n* VMH download service at https://webdav-r3lab.uni.lu/public/msp\n* BiGG web service at http://bigg.ucsd.edu/api/v2\n* MetaNetX download service at http://www.metanetx.org/cgi-bin/mnxget/mnxref\n* KEGG web service at http://rest.kegg.jp\n\nVMH notes\n^^^^^^^^^\n\nCobraBabel uses the most recent versions of `Recon2 and AGORA\n`_.\n\nVMH provides a SEED2VMH_translation.csv file which is not the same as the translation table\nin Supplementary Table 15 in the AGORA paper. Supplementary Table 15 is provided as an\nExcel workbook which was parsed into two files: (1) vmh_metabolite_xref.tsv and\n(2) vmh_reaction_xref.tsv which are provided in the \"data\" folder.\n\nBiGG Notes\n^^^^^^^^^^\n\nCobraBabel uses `BiGG API version 2 `_.\n\nUniversal metabolites can have more than one formula if different models use a\ndifferent formula for a metabolite with the same ID (same situation can occur\nwith charge). Currently, CobraBabel blindly picks the first formula in the list\nof formulae for a universal metabolite.\n\nUniversal metabolites have a list of all the compartments where the metabolite\nis used but a compartment name is not provided. Since different models may use\ndifferent names for the same compartment ID, when a universal metabolite is\nadded to a model the compartment name is not set.\n\nThere is no bulk download of universal metabolites and reactions so creating a\nuniversal model is very slow because each metabolite and reaction is downloaded\nseparately.\n\nMetaNetX Notes\n^^^^^^^^^^^^^^\n\nCobraBabel uses `MNXref Version 2017/05/04 `_.\n\nThe list of metabolites is very large and includes metabolites that are not used\nin any reaction. CobraBabel only includes metabolites that are used in a reaction\nwhen creating a universal model.\n\nSome reactions are defined with unspecified stoichiometry coefficients. For example,\nreaction MNXR109485 has the equation:\n``(2n) MNXM17@MNXD1 + 1 MNXM18575@MNXD1 = 1 MNXM1@MNXD1 + (n) MNXM47@MNXD1 + (n) MNXM87@MNXD1``.\nCurrently, CobraBabel does not include these reactions when creating a universal model.\n\nA reaction equation is defined with metabolites in a generic compartment using\nthe syntax ``MNXM17@MNXD1`` to identify the metabolite and compartment. CobraBabel\nreplaces the \"@\" character with an \"_\" character in the metabolite ID when creating\na universal model.\n\nIf a reaction has a value in the Source field, there is only one source in the\nformat: ``source:id``. Sources include Rhea (rhea), KEGG (kegg), MetaCyc (metacyc),\nUniPathway (upa), The Seed (seed), BiGG (bigg), BioPath (biopath), and Reactome\n(reactome). Set the ``verbose`` parameter when calling ``create_metanetx_universal_model()``\nto show a warning for reactions with an invalid format in the Source field.\n\nThere are no names for reactions so the reaction name is set to the reaction ID.\n\nAll reactions are defined as bi-directional so the lower and upper bounds are\nset to the default values ``(-1000.0, 1000.0)`` for all reactions.\n\nKEGG Notes\n^^^^^^^^^^\n\nCobraBabel uses the current version of the `KEGG API `_.\n\nNote, there are some limitations on using the KEGG API, most importantly:\n\n **Restrictions:** KEGG API is provided for academic use by academic users\n belonging to academic institutions. This service should not be used for bulk\n data downloads. Please obtain KEGG FTP academic subscription for downloading\n KEGG data.\n\n -- www.kegg.jp\n\nWhen setting OTU representatives in the organism database, there can be variability\nin which organism is selected when there are multiple equally good matches. For\nexample, in the KEGG database there are two Mycobacterium tuberculosis H37Rv\norganisms, one with ID \"T00015\" and one with ID \"T02178\". It is random as to which\none gets picked as the OTU representative.\n\nA sample OTU representative source file is provided in the \"data/otu-reps.tsv\" file\nwhich was retrieved from the KBase Central Data Model using the all_entities_OTU\ncommand.\n\nRelease Notes\n-------------\n\nVersion 0.1.3 (August 4, 2017)\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n* Updated create_metanetx_universal_model() to support MetaNetX/MNXref Version 3.0\n including new InChIKey value for metabolites and fully compartmentalized reactions\n (see `#1 `_)\n* Fixed setting numeric fields in MetaNetX metabolites (see\n `#2 `_)\n* Fixed failing tests due to missing comma (see\n `#3 `_)\n* Added support for DBLINKS field in KEGG Reaction database entry\n\nVersion 0.1.2 (June 13, 2017)\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n* Updated compare_model() with better comparison of reaction definition and better\n output formatting\n\nVersion 0.1.1 (June 7, 2017)\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n* Added more details on how models are compared\n\nVersion 0.1.0 (May 30, 2017)\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n* Initial version\n\nReferences\n----------\n\n1. `COBRApy: COnstraints-Based Reconstruction and Analysis for Python `_\n2. `A community-driven global reconstruction of human metabolism `_\n3. `Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota `_\n4. `BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models `_\n5. `MetaNetX.org: a website and repository for accessing, analyzing, and manipulating metabolic networks `_\n6. `KEGG: Kyoto Encyclopedia of Genes and Genomes `_\n7. `Systems Biology Knowledgebase `_\n", "description_content_type": null, "docs_url": null, "download_url": "https://pypi.python.org/pypi/cobrababel", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/mmundy42/cobrababel", "keywords": "metabolism biology optimization flux balance analysis fba", "license": "BSD", "maintainer": "", "maintainer_email": "", "name": "cobrababel", "package_url": "https://pypi.org/project/cobrababel/", "platform": "GNU/Linux", "project_url": "https://pypi.org/project/cobrababel/", "project_urls": { "Download": "https://pypi.python.org/pypi/cobrababel", "Homepage": "https://github.com/mmundy42/cobrababel" }, "release_url": "https://pypi.org/project/cobrababel/0.1.3/", "requires_dist": null, "requires_python": "", "summary": "CobraBabel: COBRA Model Translator", "version": "0.1.3" }, "last_serial": 3073044, "releases": { "0.1.0": [ { "comment_text": "", "digests": { "md5": "40469090b5602408f2eb2d988c2db882", "sha256": "1297aba5413dd25ae467aa58aa7533dcd7338e608de696dab8c3dfbef22765cc" }, "downloads": -1, "filename": "cobrababel-0.1.0.tar.gz", "has_sig": false, "md5_digest": "40469090b5602408f2eb2d988c2db882", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 28336, "upload_time": "2017-05-30T16:03:50", "url": "https://files.pythonhosted.org/packages/f5/fb/5537b002cc580e4e4f81a25f4c586df7deeeeab9358e579bc75820735979/cobrababel-0.1.0.tar.gz" } ], "0.1.1": [ { "comment_text": "", "digests": { "md5": "e1449c287a02a75f751b8ca5f6b8a8fa", "sha256": "0a5086bba7edeec0c4a948f2df699b0b23390dd70af93bd10c6cae7d91a83528" }, "downloads": -1, "filename": "cobrababel-0.1.1.tar.gz", "has_sig": false, "md5_digest": "e1449c287a02a75f751b8ca5f6b8a8fa", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 29105, "upload_time": "2017-06-07T19:25:14", "url": "https://files.pythonhosted.org/packages/89/09/13554a3390fce886ac5d1f07450ccb9840ae5ceef2205ad8630454272171/cobrababel-0.1.1.tar.gz" } ], "0.1.2": [ { "comment_text": "", "digests": { "md5": "24b9174f485dbeffbd37dbfbe90be67c", "sha256": "64cb0c5415fe9c1c66a4309135ac1513f423f324d66b43102f3822ac20fb16e9" }, "downloads": -1, "filename": "cobrababel-0.1.2.tar.gz", "has_sig": false, "md5_digest": "24b9174f485dbeffbd37dbfbe90be67c", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 29189, "upload_time": "2017-06-13T16:22:21", "url": "https://files.pythonhosted.org/packages/0a/d2/020eb42cf255dda9aa4e29ab0287b58036d799a0457bd2f012afb1adc1a8/cobrababel-0.1.2.tar.gz" } ], "0.1.3": [ { "comment_text": "", "digests": { "md5": "f2795217b5117b28de1ffbb80c67fd2f", "sha256": "0319dbf6f8e3e816371ce672e78cbc26676e211bc203a1f1c4adf8c45bdfc4d4" }, "downloads": -1, "filename": "cobrababel-0.1.3.tar.gz", "has_sig": false, "md5_digest": "f2795217b5117b28de1ffbb80c67fd2f", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 30906, "upload_time": "2017-08-04T15:57:33", "url": "https://files.pythonhosted.org/packages/11/36/764850dd692ad65eb6069ac7d446d81c3b5dd5b75c044ef2bb778b9f8cff/cobrababel-0.1.3.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "f2795217b5117b28de1ffbb80c67fd2f", "sha256": "0319dbf6f8e3e816371ce672e78cbc26676e211bc203a1f1c4adf8c45bdfc4d4" }, "downloads": -1, "filename": "cobrababel-0.1.3.tar.gz", "has_sig": false, "md5_digest": "f2795217b5117b28de1ffbb80c67fd2f", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 30906, "upload_time": "2017-08-04T15:57:33", "url": "https://files.pythonhosted.org/packages/11/36/764850dd692ad65eb6069ac7d446d81c3b5dd5b75c044ef2bb778b9f8cff/cobrababel-0.1.3.tar.gz" } ] }