{"id":18418984,"url":"https://github.com/smrfeld/physics-based-ml-reaction-networks","last_synced_at":"2026-03-19T04:17:09.369Z","repository":{"id":115478534,"uuid":"370174157","full_name":"smrfeld/physics-based-ml-reaction-networks","owner":"smrfeld","description":"Code for paper \"Physics-based machine learning for modeling IP3 induced calcium oscillations\" - DOI: 10.5281/zenodo.4839127","archived":false,"fork":false,"pushed_at":"2021-05-29T18:56:40.000Z","size":16661,"stargazers_count":2,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-10-24T21:28:59.132Z","etag":null,"topics":["chemistry","machine-learning","physics-based","physics-based-ml","physics-informed","physics-informed-ml","reaction-networks","reactions"],"latest_commit_sha":null,"homepage":"","language":"Mathematica","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/smrfeld.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-05-23T23:01:21.000Z","updated_at":"2024-06-07T00:02:03.000Z","dependencies_parsed_at":null,"dependency_job_id":"d7a704c1-373a-48ef-bf26-775527e6902e","html_url":"https://github.com/smrfeld/physics-based-ml-reaction-networks","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/smrfeld/physics-based-ml-reaction-networks","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smrfeld%2Fphysics-based-ml-reaction-networks","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smrfeld%2Fphysics-based-ml-reaction-networks/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smrfeld%2Fphysics-based-ml-reaction-networks/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smrfeld%2Fphysics-based-ml-reaction-networks/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/smrfeld","download_url":"https://codeload.github.com/smrfeld/physics-based-ml-reaction-networks/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smrfeld%2Fphysics-based-ml-reaction-networks/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29703747,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-21T23:35:04.139Z","status":"online","status_checked_at":"2026-02-22T02:00:08.193Z","response_time":110,"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":["chemistry","machine-learning","physics-based","physics-based-ml","physics-informed","physics-informed-ml","reaction-networks","reactions"],"created_at":"2024-11-06T04:15:16.772Z","updated_at":"2026-02-22T02:33:21.196Z","avatar_url":"https://github.com/smrfeld.png","language":"Mathematica","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Physics-based machine learning for modeling IP3 induced calcium oscillations\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4839127.svg)](https://doi.org/10.5281/zenodo.4839127)\n\nThis repo. contains the code for the paper `Physics-based machine learning for modeling IP3 induced calcium oscillations`.\n\n\u003cimg src=\"figures_readme/fig_1.png\" alt=\"drawing\" width=\"600\"/\u003e\n\n## Contents\n\n* [learn_ip3](learn_ip3) - Models extrapolating in `IP3` for a single volume and number of `IP3Rs` (`IP3` receptors).\n* [learn_ip3r](learn_ip3r) - Models extrapolating in the number of `IP3Rs` for a single volume, across all `IP3` values.\n* [stochastic_simulations](stochastic_simulations) - Stochastic simulations for generating training data for both models.\n\nThe code is a mix of `Mathematica` notebooks and `C++`.\n\n## Data\n\nAll data is stored using [DVC (data version control)](https://dvc.org). You need to install DVC, then you should be able to just run from this directory:\n```\ndvc pull\n```\nto get all the data. \n\n**BE AWARE** that this can be a lot to download, particularly because of the [stochastic_simulations](stochastic_simulations) - otherwise you can look for the `.dvc` files in the various directory and load those individually.\n\n## Figures\n\n\u003cimg src=\"figures_readme/fig_2.png\" alt=\"drawing\" width=\"600\"/\u003e\n\u003cimg src=\"figures_readme/fig_3.png\" alt=\"drawing\" width=\"600\"/\u003e\n\u003cimg src=\"figures_readme/fig_4.png\" alt=\"drawing\" width=\"600\"/\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmrfeld%2Fphysics-based-ml-reaction-networks","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsmrfeld%2Fphysics-based-ml-reaction-networks","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmrfeld%2Fphysics-based-ml-reaction-networks/lists"}