{"id":44257539,"url":"https://github.com/compomics/pride-asa-pipeline","last_synced_at":"2026-02-10T16:36:03.786Z","repository":{"id":33881808,"uuid":"37592837","full_name":"CompOmics/pride-asa-pipeline","owner":"CompOmics","description":"Uniform annotation of identified spectra.","archived":false,"fork":false,"pushed_at":"2021-10-12T10:22:31.000Z","size":170269,"stargazers_count":1,"open_issues_count":1,"forks_count":1,"subscribers_count":17,"default_branch":"master","last_synced_at":"2025-09-10T05:09:44.193Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Java","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/CompOmics.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE-2.0.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2015-06-17T12:13:32.000Z","updated_at":"2023-09-14T05:39:46.000Z","dependencies_parsed_at":"2022-07-13T15:31:07.657Z","dependency_job_id":null,"html_url":"https://github.com/CompOmics/pride-asa-pipeline","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/CompOmics/pride-asa-pipeline","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CompOmics%2Fpride-asa-pipeline","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CompOmics%2Fpride-asa-pipeline/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CompOmics%2Fpride-asa-pipeline/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CompOmics%2Fpride-asa-pipeline/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CompOmics","download_url":"https://codeload.github.com/CompOmics/pride-asa-pipeline/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CompOmics%2Fpride-asa-pipeline/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29307920,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-10T16:09:25.305Z","status":"ssl_error","status_checked_at":"2026-02-10T16:08:52.170Z","response_time":65,"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":"2026-02-10T16:36:03.106Z","updated_at":"2026-02-10T16:36:03.776Z","avatar_url":"https://github.com/CompOmics.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"# pride-asa-pipeline\n![logo](http://genesis.ugent.be/uvpublicdata/pride-asa-pipeline/pride-asa-pipeline-logo.png) \n\n * [Project Description](#project-description)\n * [Downloads](#downloads)\n * [Usage](#usage)\n * [Troubleshooting](#troubleshooting)\n * [Related Projects](#related-projects)\n * [Project Support](#project-support)\n\n----\n\n## Project Description\n\nPride-asap is a library written in Java that provides a uniform annotation of identified spectra stored in PRIDE. The application can be ran in a command line mode for automated processing of multiple PRIDE experiments, but also has a graphical user interface that allows end users to annotate the spectra in PRIDE experiments and to inspect the results in detail.\n\n### Citation\n * [Hulstaert et al: J Proteomics. 2013 Apr 17. pii: S1874-3919(13)00192-9](http://www.ncbi.nlm.nih.gov/pubmed/23603108)\n * If you use pride-asa-pipeline as part of a paper, please include the reference above.\n\n[Go to top of page](#pride-asa-pipeline)\n\n----\n\n## Downloads\n\nDownload pride-asa-pipeline 1.5.11 [here](https://genesis.ugent.be/maven2/com/compomics/pride-asa-pipeline/1.5.11/pride-asa-pipeline-1.5.11.zip). \n\n\n[Go to top of page](#pride-asa-pipeline)\n\n----\n\n## Usage\n\nThe pride-asa-pipeline jar file and all the libraries needed to run the tool. Double clicking this resulting jar file will start the pipeline. See the [manual](https://github.com/compomics/pride-asa-pipeline/wiki/Manual) for additional information on how to run and configure the pipeline.\n\n[Go to top of page](#pride-asa-pipeline)\n\n----\n\n## Troubleshooting\n\nPlease report any issues or requests in the [issues section](https://github.com/compomics/pride-asa-pipeline/issues). We will attempt to come up with a solution as soon as possible.\n\n[Go to top of page](#pride-asa-pipeline)\n\n----\n\n## Related Projects\n\nThe pride-asa-pipeline makes use of [compomics-utilities](http://code.google.com/p/compomics-utilities).\n\nYou might also find some of the following projects interesting: [Peptizer](http://code.google.com/p/peptizer), [dbtoolkit](https://github.com/compomics/dbtoolkit),\n[ms-lims](http://code.google.com/p/ms-lims),\n[Rover](http://code.google.com/p/compomics-rover) and\n[PeptideShaker](http://code.google.com/p/peptide-shaker).\n\n[Go to top of page](#pride-asa-pipeline)\n\n----\n\n## Project Support\n\nThe pride-asa-pipeline project is grateful for the support by:\n\n| Compomics | VIB | Ghent University|\n|:--:|:--:|:--:|\n| [![compomics](http://genesis.ugent.be/uvpublicdata/image/compomics.png)](http://www.compomics.com) | [![vib](http://genesis.ugent.be/uvpublicdata/image/vib.png)](http://www.vib.be) | [![ugent](http://genesis.ugent.be/uvpublicdata/image/ugent.png)](http://www.ugent.be/en) |\n\n[Go to top of page](#pride-asa-pipeline)\n\n----\n\n| IntelliJ | Netbeans | Java | Maven |\n|:--:|:--:|:--:|:--:|\n| [![intellij](https://www.jetbrains.com/idea/docs/logo_intellij_idea.png)](https://www.jetbrains.com/idea/) | [![netbeans](https://netbeans.org/images_www/visual-guidelines/NB-logo-single.jpg)](https://netbeans.org/) | [![java](http://genesis.ugent.be/uvpublicdata/image/java.png)](http://java.com/en/) | [![maven](http://genesis.ugent.be/uvpublicdata/image/maven.png)](http://maven.apache.org/) |\n\n[Go to top of page](#pride-asa-pipeline)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcompomics%2Fpride-asa-pipeline","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcompomics%2Fpride-asa-pipeline","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcompomics%2Fpride-asa-pipeline/lists"}