{"id":24529935,"url":"https://github.com/mschubert/biomodels_curation","last_synced_at":"2025-06-11T02:38:57.610Z","repository":{"id":1916050,"uuid":"2843679","full_name":"mschubert/biomodels_curation","owner":"mschubert","description":"Scripts used for curation of Blood Coagulation models for the BioModels database","archived":false,"fork":false,"pushed_at":"2013-04-11T11:57:22.000Z","size":576,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-22T07:53:00.526Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mschubert.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2011-11-24T13:55:23.000Z","updated_at":"2013-12-03T22:15:52.000Z","dependencies_parsed_at":"2022-09-07T02:20:42.622Z","dependency_job_id":null,"html_url":"https://github.com/mschubert/biomodels_curation","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mschubert%2Fbiomodels_curation","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mschubert%2Fbiomodels_curation/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mschubert%2Fbiomodels_curation/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mschubert%2Fbiomodels_curation/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mschubert","download_url":"https://codeload.github.com/mschubert/biomodels_curation/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243770839,"owners_count":20345356,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-01-22T07:53:06.270Z","updated_at":"2025-03-15T18:21:01.031Z","avatar_url":"https://github.com/mschubert.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"BioModels curation scripts\n==========================\n\nThis is a collection of scripts that were used to curate Blood Coagulation\nmodels. Those were taken from various scientific articles and encoded in\nthe [Systems Biology Markup Language][sbml] (SBML) and subsequently annotated\nwith identifiers from e.g. [UniProt][uniprot], so that the model entities\ncould be linked to physical ones. Additionally, one or more figures from the \noriginal article were reproduced in order to validate the model and its\nsimulation results.\n\nNote that the models deposited in the [BioModels database][bmdb] will always \nbe more complete and up-to-date than the ones provided here. If plan on using \nthe models instead of the curation framework, please use them from the database\ndirectly.\n\nAll models published in the BioModels database are released without copyright\nunder a [CC0][cc0] license. The Framework is (c) [EMBL][embl], 2011 but may\nbe used under the terms of the [GPL][gpl] version 2 or later.\n\nUsage\n-----\n\nThe sample models are provided either as Copasi or unannotated SBML files.\nUsing the Make framework, they are transformed into annotated SBML files and\nthose are plotted using specific plotting scripts. To run, type:\n\n    ./configure\n    make\n\nUpon which all model files and figures are created. Note that you can run\n`make` in only one subdirectory as well, `configure` needs to be called before,\nhowever.\n\nRequirements\n------------\n\nThe following software is required to successfully run the curation framework\nwith the sample models provided:\n\n * [Python][python]\n                - A high-level scripting language that can be used for rapid\n                  development and comes a lot of functionality included. Extra\n                  libraries required are [NumPy][numpy] (for numerical data \n                  structures), [matplotlib][matplotlib] (for plotting), \n                  [libSBML][libsbml] (for manipulation of SBML files), \n                  [SymPy][sympy] (for matching of kinetic laws to \n                  [SBO terms][sbo]) and [SUDS][suds] (for interacting with the \n                  SBO webservice via [SOAP][soap]).\n * [Coapsi][copasi]\n                - An application for simulation and analysis of biochemical\n                  networks and their dynamics. It is a stand-alone application \n                  that comes with a command-line (CopasiSE) and GUI (CopasiUI) \n                  version and supports the [SBML][sbml] standard. The program\n                  needs to be compiled with Python bindings enabled.\n * [HTML Tidy][tidy]\n                - An application to clean up HTML and XML formatting. This\n                  tool is used to format the SBML files nicely after \n                  annotation.\n\nSample models\n-------------\n\nIn the course of the curation project, about 30 models were curated for the\nBioModels database. Some from the following five articles are provided as\nsample files for the framework here:\n\n * K. C. Jones and K. G. Mann. A model for the tissue factor pathway to \n   thrombin. II. a mathematical simulation. Journal of Biological Chemistry, \n   269(37):23367, 1994.\n * M. F. Hockin, K. C. Jones, S. J. Everse, and K. G. Mann. A model for the\n   stoichiometric regulation of blood coagulation. Journal of Biological \n   Chemistry, 277(21):18322-18333, 2002.\n * S. D. Bungay, P. A. Gentry, and R. D. Gentry. A mathematical model of lipid-\n   mediated thrombin generation. Mathematical Medicine and Biology, 20(1):105-\n   129, 2003.\n * T. Wajima, G. K. Isbister, and S. B. Duffull. A comprehensive model for the\n   humoral coagulation network in humans. Clinical Pharmacology and \n   Therapeutics, 86(3):290–298, 2009.\n * C. J. Lee, S. Wu, C. Eun, and L. G. Pedersen. A revisit to the one form \n   kinetic model of prothrombinase. Biophysical chemistry, 149(1-2):28–33, 2010.\n\n[sbml]: http://sbml.org/Basic_Introduction_to_SBML\n[uniprot]: http://www.uniprot.org/\n[embl]: http://www.embl.de/\n[bmdb]: http://www.ebi.ac.uk/biomodels-main/\n[gpl]: http://www.gnu.org/licenses/gpl.html\n[cc0]: http://creativecommons.org/publicdomain/zero/1.0/\n[python]: http://python.org/\n[copasi]: http://www.copasi.org/tiki-view_articles.php\n[tidy]: http://tidy.sourceforge.net/\n[numpy]: http://numpy.scipy.org/\n[matplotlib]: http://matplotlib.sourceforge.net/\n[libsbml]: http://sbml.org/Software/libSBML\n[sympy]: http://code.google.com/p/sympy/\n[sbo]: http://www.ebi.ac.uk/sbo/main/\n[suds]: https://fedorahosted.org/suds/\n[soap]: http://de.wikipedia.org/wiki/SOAP\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmschubert%2Fbiomodels_curation","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmschubert%2Fbiomodels_curation","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmschubert%2Fbiomodels_curation/lists"}