{"id":37610706,"url":"https://github.com/adicksonlab/wepy-analysis","last_synced_at":"2026-01-16T10:20:11.747Z","repository":{"id":298942185,"uuid":"1001622947","full_name":"ADicksonLab/wepy-analysis","owner":"ADicksonLab","description":"Analysis tools for wepy simulations","archived":false,"fork":false,"pushed_at":"2025-07-31T14:50:18.000Z","size":61,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-09-08T23:58:06.167Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","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/ADicksonLab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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,"zenodo":null}},"created_at":"2025-06-13T17:47:10.000Z","updated_at":"2025-07-31T14:50:21.000Z","dependencies_parsed_at":"2025-07-21T16:12:12.448Z","dependency_job_id":"9fe832a6-944b-4cce-b299-da6cf2940846","html_url":"https://github.com/ADicksonLab/wepy-analysis","commit_stats":null,"previous_names":["adicksonlab/wepy-analysis"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/ADicksonLab/wepy-analysis","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ADicksonLab%2Fwepy-analysis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ADicksonLab%2Fwepy-analysis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ADicksonLab%2Fwepy-analysis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ADicksonLab%2Fwepy-analysis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ADicksonLab","download_url":"https://codeload.github.com/ADicksonLab/wepy-analysis/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ADicksonLab%2Fwepy-analysis/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28478049,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T06:30:42.265Z","status":"ssl_error","status_checked_at":"2026-01-16T06:30:16.248Z","response_time":107,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":"2026-01-16T10:20:10.948Z","updated_at":"2026-01-16T10:20:11.690Z","avatar_url":"https://github.com/ADicksonLab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# WepyAnalysis\n\nWepyAnalysis is a modular toolkit for analyzing data generated from Weighted Ensemble (WE) simulations using the [Wepy](https://github.com/ADicksonLab/wepy) framework.\n\nThe codebase is organized into five main components:\n- `featurization/`: Tools for extracting structural features from WE data\n- `dataset/`: Code for generating datasets from WE data\n- `msm/`: Building Markov State Models (MSMs) and performing kinetic analysis\n- `example/`: Example scripts for running simulations with Wepy and building MSMs\n\nThis repository is under active development and intended for researchers working with WE data, especially those using the Wepy framework.\n\n\n## Installation\n\nWe recommend installing WepyAnalysis with a Python package manager such as conda or mamba. The package is tested and fully compatible with ```Python 3.12```, and we strongly encourage using ```python\u003e=3.10``` for compatibility.\n\n```\nconda create -n wepy-analysis python=3.12\nconda activate wepy-analysis\n```\n\nOnce your python environment is ready, `wepy-analysis` can be installed with `pip` as follows:\n\n```\npip install git+https://github.com/ADicksonLab/wepy-analysis\n```\n\nwhich will also install all dependencies. The installation procedure takes less than a minute to complete at a local desktop.\n\n## Dependencies:\n\n```\nWepy (https://github.com/ADicksonLab/wepy) \u003e= 1.2\ngeomm (https://github.com/ADicksonLab/geomm) \u003e= 0.3\ncsnanalysis (https://github.com/ADicksonLab/CSNAnalysis) \u003e= 0.6.0\nnumpy \u003e= 2.3.1\nscipy \u003e= 1.16.0\nh5py \u003e= 3.14.0\nmdtraj \u003e= 1.11.0\nscikit-learn \u003e= 1.7.0\ndeeptime \u003e= 0.4.5\n```\n\n## More Information\n- Example dataset files can be found at current [Zenodo DOI](https://zenodo.org/records/15361245)\n- This repository is a part of the preprint [\"Determinants of Improved CGRP Peptide Binding Kinetics Revealed by Enhanced Molecular Simulations\"](https://www.biorxiv.org/content/10.1101/2025.06.13.659569v1) and can be used to build MSMs explained in the paper. \n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fadicksonlab%2Fwepy-analysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fadicksonlab%2Fwepy-analysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fadicksonlab%2Fwepy-analysis/lists"}