{"id":19197318,"url":"https://github.com/lolab-msm/corm","last_synced_at":"2025-10-13T16:14:09.773Z","repository":{"id":24388337,"uuid":"27788241","full_name":"LoLab-MSM/CORM","owner":"LoLab-MSM","description":"COX2 Reaction Model","archived":false,"fork":false,"pushed_at":"2017-02-28T20:17:55.000Z","size":28910,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":13,"default_branch":"master","last_synced_at":"2025-10-13T16:14:08.945Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","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/LoLab-MSM.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":"2014-12-09T21:30:56.000Z","updated_at":"2019-07-23T06:16:11.000Z","dependencies_parsed_at":"2022-08-25T17:00:25.648Z","dependency_job_id":null,"html_url":"https://github.com/LoLab-MSM/CORM","commit_stats":null,"previous_names":["lolab-vu/corm"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/LoLab-MSM/CORM","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LoLab-MSM%2FCORM","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LoLab-MSM%2FCORM/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LoLab-MSM%2FCORM/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LoLab-MSM%2FCORM/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LoLab-MSM","download_url":"https://codeload.github.com/LoLab-MSM/CORM/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LoLab-MSM%2FCORM/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279016061,"owners_count":26085798,"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","status":"online","status_checked_at":"2025-10-13T02:00:06.723Z","response_time":61,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":"2024-11-09T12:16:21.587Z","updated_at":"2025-10-13T16:14:09.720Z","avatar_url":"https://github.com/LoLab-MSM.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"COX-2 Reaction Model (CORM)\n=============\n\nCORM provides a proposed model of cyclooxygenase-2 (COX-2) allosteric and catalytic interactions with arachidonic acid (AA) and 2-arachidonoylglycerol (2-AG).\nCOX-2 turnover of AA or 2-AG produces prostaglandins (PGs) or prostaglandin glyceryl esters (PG-Gs), respectively.\n\nQuickstart\n----------\n\nTo facilitate easy use of CORM, we provide a virtual machine with everything you need to run CORM already installed.  You can download it [here](http://puma.mc.vanderbilt.edu:8000/virtual_machines/CORM_demo.ova). Warning: 1.4G file.\n\nInstallation\n------------\n\nCORM is encoded as a Python Systems Biology (PySB) model.  To download and install PySB and its dependencies, [see the PySB documentation](http://docs.pysb.org/en/latest/installation.html#option-2-installing-the-dependencies-yourself).\n\nIf you would like to run Bayesian Markov Chain Monte Carlo (MCMC) fitting of the CORM parameters, you will also need the LoLab-VU fork of PyMC 3.\n\nClone the repository:\n```\ngit clone https://github.com/LoLab-VU/pymc\n```\n\nEnter the cloned directory and switch to the branch that has the DREAM MCMC stepping method:\n```\ngit checkout dream\n```\n\nThen install PyMC:\n```\npython setup.py install\n```\n\nRunning CORM\n------------\n\nThe CORM model file is defined in the file [corm.py](https://github.com/LoLab-VU/CORM/blob/master/corm.py).\n\nYou can import the model for exploration by typing:\n```python\nfrom corm import model\n```\nfrom an iPython session.\n\nWe also provide an iPython notebook that will walk you through how CORM is defined [here](http://nbviewer.ipython.org/urls/raw.githubusercontent.com/LoLab-VU/CORM/master/corm_tutorial.ipynb).\n\nFitting CORM Parameters\n-----------------------\n\nThe file [run_pymc_sampling.py](https://github.com/LoLab-VU/CORM/blob/master/run_pymc_sampling.py) provides a Python script for fitting CORM parameters using PyMC.\n\nTo run the fitting, simply type:\n```\npython run_pymc_sampling.py\n```\n\nParameter traces for all MCMC chains will be saved to a pickled Python dictionary as specified in run_pymc_sampling.py. \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flolab-msm%2Fcorm","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flolab-msm%2Fcorm","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flolab-msm%2Fcorm/lists"}