{"id":18669972,"url":"https://github.com/blahah/biopsy","last_synced_at":"2025-09-13T10:39:04.864Z","repository":{"id":8630519,"uuid":"10276286","full_name":"blahah/biopsy","owner":"blahah","description":"Biopsy - the Bioinformatic Optimisation System","archived":false,"fork":false,"pushed_at":"2015-11-01T23:22:04.000Z","size":5987,"stargazers_count":16,"open_issues_count":6,"forks_count":3,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-07-27T11:42:06.882Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Ruby","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":"stanfordnlp/CoreNLP","license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/blahah.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}},"created_at":"2013-05-24T22:37:01.000Z","updated_at":"2023-07-21T21:45:46.000Z","dependencies_parsed_at":"2022-09-01T08:00:11.586Z","dependency_job_id":null,"html_url":"https://github.com/blahah/biopsy","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/blahah/biopsy","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/blahah%2Fbiopsy","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/blahah%2Fbiopsy/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/blahah%2Fbiopsy/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/blahah%2Fbiopsy/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/blahah","download_url":"https://codeload.github.com/blahah/biopsy/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/blahah%2Fbiopsy/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274949944,"owners_count":25379535,"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":"2025-09-13T02:00:10.085Z","response_time":70,"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":"2024-11-07T08:49:21.779Z","updated_at":"2025-09-13T10:39:04.830Z","avatar_url":"https://github.com/blahah.png","language":"Ruby","funding_links":[],"categories":[],"sub_categories":[],"readme":"biopsy\n==========\n\n[![Gem Version](https://badge.fury.io/rb/biopsy.png)][gem]\n[![Build Status](https://secure.travis-ci.org/Blahah/biopsy.png?branch=master)][travis]\n[![Dependency Status](https://gemnasium.com/Blahah/biopsy.png?travis)][gemnasium]\n[![Code Climate](https://codeclimate.com/github/Blahah/biopsy.png)][codeclimate]\n[![Coverage Status](https://coveralls.io/repos/Blahah/biopsy/badge.png?branch=master)][coveralls]\n\n[gem]: https://badge.fury.io/rb/biopsy\n[travis]: https://travis-ci.org/Blahah/biopsy\n[gemnasium]: https://gemnasium.com/Blahah/biopsy\n[codeclimate]: https://codeclimate.com/github/Blahah/biopsy\n[coveralls]: https://coveralls.io/r/Blahah/biopsy\n\nAn automatic optimisation framework for programs and pipelines.\n\nBiopsy is a framework for optimising the settings of any program or pipeline which produces a measurable output. It is particularly intended for bioinformatics, where computational pipelines take a long time to run, making optimisation of parameters using crude methods unfeasible. Biopsy will use a range of discrete optimisation strategies to rapidly find the settings that perform the best.\n\nIt can handle parameter spaces of any size: if it is possible to try every parameter combination in the time you have available, Biopsy will do this. However, Biopsy really shines when handling large numbers of parameter combinations.\n\n## Development status\n\nThis project is in early development and is not yet ready for deployment.\nPlease don't report issues or request documentation until we are ready for release. If you have a burning desire to use biopsy, get in touch: rds45@cam.ac.uk.\n\n## Installation\n\nMake sure you have Ruby installed, then:\n\n`gem install biopsy`\n\n## Usage\n\nDetailed usage instructions are on the wiki. Here's a quick overview:\n\n1. Define your optimisation target. This is a program or pipeline you want to optimise, and you define it by filling in a template YAML file and wrapping your program in a tiny Ruby launcher.\n2. Define your objective function. This is a program that analyses the output of your program and gives it a score. You define it by writing a small amount of Ruby code. Don't worry - there's a template and detailed instructions on the wiki.\n3. Run Biopsy, and wait while the experiment runs. Maybe grab a cup of tea, read some [hacker news](http://news.ycombinator.com).\n4. Bask in the brilliance of your new optimal settings.\n\n### Command line examples\n\n`biopsy list targets`\n`biopsy list objectives`\n`biposy run --target test_target --objective test_objective --input test_file.txt --time-limit 24h`\n\n### Optimisation algorithms\n\n1. Parameter Sweeper - a simple combinatorial parameter sweep, with optional subsampling of the parameter space\n2. Tabu Search - a local search with a long memory that takes the consensus of multiple searchers\n3. SPEA2 - a high performance general-purpose genetic algorithm\n\n### Documentation\n\nDocumentation is in development and will be released with the beta.\n\n### Citation\n\nThis is *pre-release*, *pre-publication* academic software. In lieu of a paper to cite, please cite this Github repo and/or the [Figshare DOI (http://dx.doi.org/10.6084/m9.figshare.790660\n)](http://dx.doi.org/10.6084/m9.figshare.790660) if your use of the software leads to a publication.\n\n[![Analytics](https://ga-beacon.appspot.com/UA-46900280-1/Blahah/biopsy)](https://github.com/Blahah/biopsy)\n\n### Software using Biopsy\n\n- [Assemblotron](https://github.com/Blahah/assemblotron) can fully optimise any *de-novo* transcriptome assembler to produce the optimal assembly possible given a particular input. This typically takes little more time than running a single assembly.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fblahah%2Fbiopsy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fblahah%2Fbiopsy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fblahah%2Fbiopsy/lists"}