{"id":22011471,"url":"https://github.com/michaelwenk/sherlock","last_synced_at":"2025-08-23T05:11:42.036Z","repository":{"id":39915101,"uuid":"315139777","full_name":"michaelwenk/sherlock","owner":"michaelwenk","description":"Web Services for Computer-Assisted Structure Elucidation (CASE)","archived":false,"fork":false,"pushed_at":"2023-06-22T05:42:35.000Z","size":74577,"stargazers_count":5,"open_issues_count":3,"forks_count":2,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-04-04T07:36:04.851Z","etag":null,"topics":["docker","nmr-spectroscopy","nmrshiftdb","pylsd","structure-elucidation"],"latest_commit_sha":null,"homepage":"","language":"Java","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/michaelwenk.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}},"created_at":"2020-11-22T21:54:30.000Z","updated_at":"2025-02-24T22:18:41.000Z","dependencies_parsed_at":"2022-08-29T09:01:47.202Z","dependency_job_id":"e52a8177-0b9c-4c51-8cf3-fca6af067416","html_url":"https://github.com/michaelwenk/sherlock","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/michaelwenk/sherlock","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/michaelwenk%2Fsherlock","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/michaelwenk%2Fsherlock/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/michaelwenk%2Fsherlock/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/michaelwenk%2Fsherlock/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/michaelwenk","download_url":"https://codeload.github.com/michaelwenk/sherlock/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/michaelwenk%2Fsherlock/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":271745492,"owners_count":24813504,"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":"2025-08-23T02:00:09.327Z","response_time":69,"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":["docker","nmr-spectroscopy","nmrshiftdb","pylsd","structure-elucidation"],"created_at":"2024-11-30T02:17:03.518Z","updated_at":"2025-08-23T05:11:42.005Z","avatar_url":"https://github.com/michaelwenk.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![DOI](https://zenodo.org/badge/315139777.svg)](https://zenodo.org/badge/latestdoi/315139777) [![License](https://img.shields.io/badge/License-MIT%202.0-blue.svg)](https://opensource.org/licenses/MIt)\n[![GitHub contributors](https://img.shields.io/github/contributors/michaelwenk/sherlock.svg)](https://github.com/michaelwenk/sherlock/graphs/contributors/) [![GitHub issues](https://img.shields.io/github/issues/michaelwenk/sherlock.svg)](https://github.com/michaelwenk/sherlock/issues/) [![GitHub release](https://img.shields.io/github/release/michaelwenk/sherlock.svg)](https://github.com/michaelwenk/sherlock/releases/)\n\n\u003cimg width=\"150\" alt=\"sherlock-logo\" src=\"public/Sherlock.png\" align=\"right\"\u003e\n\n# Sherlock\nWeb services for Computer-Assisted Structure Elucidation (CASE).\n\nA [graphical user interface](https://github.com/michaelwenk/sherlock-frontend) and [publication](https://doi.org/10.3390/molecules28031448) are available.\n\n\n\n## Core  Features\n- Dereplication\n- Elucidation\n- Retrieval of previously generated results \n\nThe dereplication, chemical shift prediction and statistical detection of structural constraints are enabled by using entries from NMRShiftDB and COCONUT containing structural and spectral properties. Spectra in use are both experimental and predicted.  \n\n[casekit](https://github.com/michaelwenk/casekit) serves as computational library within Sherlock.\n\n[PyLSD](https://github.com/nuzillard/PyLSD) is used for structure generation. \n\u003c!---\nSee [Dependencies](#dependencies) section.\n--\u003e\n\n## Docker and Execution of pre-built Containers\nThis project uses Docker containers (https://www.docker.com) and starts them via docker-compose. Make sure that docker-compose is installed.\n\nNOTE: It is recommended to set the accessible RAM to 6 GB or higher and the number of available CPU cores to two. This can be done easily in the Docker Desktop application, see [here](/public/Docker_settings.png).\n\n\n### Download\nClone this repository and change the directory:\n \n    git clone https://github.com/michaelwenk/sherlock.git\n    cd sherlock\n\nNow pull all the containers needed for execution from Docker Hub:\n\n     docker-compose -f docker-compose.yml -f docker-compose.publish.yml pull\n\n### Create and Start\nTo create the network and start the services for the first time (in detached mode) use:\n\n    docker-compose -f docker-compose.yml -f docker-compose.publish.yml up -d\n\nNote: It will take several minutes until all services are available and registered, i.e. due to the extraction of the compressed fragment data.\n\nIf the container network was already created beforehand and stopped via \"stop\" command, then the \"start\" command can be used. \nThis will avoid extracting the fragments again and the services should be ready within a few seconds.\n\n    docker-compose -f docker-compose.yml -f docker-compose.publish.yml start\n\n### Stop and Removal\nTo stop the application use:\n\n    docker-compose -f docker-compose.yml -f docker-compose.publish.yml stop\n\nIf the removal of the network created by docker-compose is desired, then use the down command:\n\n    docker-compose -f docker-compose.yml -f docker-compose.publish.yml down\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmichaelwenk%2Fsherlock","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmichaelwenk%2Fsherlock","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmichaelwenk%2Fsherlock/lists"}