{"id":19834835,"url":"https://github.com/jamesalbert/minisana","last_synced_at":"2026-05-14T17:03:59.429Z","repository":{"id":83346893,"uuid":"91508498","full_name":"jamesalbert/minisana","owner":"jamesalbert","description":"Miniature Simulated Annealing Network Aligner","archived":false,"fork":false,"pushed_at":"2017-06-20T01:42:39.000Z","size":6212,"stargazers_count":0,"open_issues_count":1,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-11-22T17:03:41.551Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"C","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/jamesalbert.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}},"created_at":"2017-05-16T22:03:10.000Z","updated_at":"2017-05-27T04:17:54.000Z","dependencies_parsed_at":"2023-03-12T18:01:24.791Z","dependency_job_id":null,"html_url":"https://github.com/jamesalbert/minisana","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/jamesalbert/minisana","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jamesalbert%2Fminisana","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jamesalbert%2Fminisana/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jamesalbert%2Fminisana/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jamesalbert%2Fminisana/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jamesalbert","download_url":"https://codeload.github.com/jamesalbert/minisana/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jamesalbert%2Fminisana/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33034788,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-13T13:14:54.681Z","status":"online","status_checked_at":"2026-05-14T02:00:06.663Z","response_time":57,"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":"2024-11-12T12:05:42.969Z","updated_at":"2026-05-14T17:03:59.424Z","avatar_url":"https://github.com/jamesalbert.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"# minisana\nMiniature Simulated Annealing Network Aligner\n\n[![Build Status](https://travis-ci.org/jamesalbert/minisana.svg?branch=master)](https://travis-ci.org/jamesalbert/minisana)\n[![Coverage Status](https://coveralls.io/repos/github/jamesalbert/minisana/badge.svg?branch=master)](https://coveralls.io/github/jamesalbert/minisana?branch=master)\n\n\u003cimg src=\"http://i.imgur.com/tSLzyQg.png\" width=\"550px\"\u003e\n\n## Install\n\nRunning `make` will do a few things:\n\n  1. compile object files in `_objs`\n  2. build the binary `bin/mini`\n  3. build the shared library `lib/libmini.so`\n  4. create empty directories `output` where .json files will be stored\n\n## Tests\n\nRun tests with `make test`. Along with showing the test results, a coverage report will be generated as coverage/report.html. Open the report in your browser to see the total code coverage. `make docker` will also run the tests during image creation.\n\n## Docker\n\nYou can build a minisana image with `make docker` or go straight to running it with:\n\n```sh\nMINIOPTS=\"-n input/yeast.gw -N input/human.gw -t 10000000\" make docker_run\n```\n\nThen you can check the logs with `docker logs -f \u003ccontainer-id\u003e`. Once it's finished, you can check the json file written to `~/output`.\n\n## Usage\n\n```sh\n./bin/mini -n,-N [-s,-a,-o,-t]\n\n  -n: path to the smaller network\n  -N: path to the bigger network (small n, big N... get it?)\n  -s: path to sequence file [defaults to \"input/yeast_human.bitscores\"]\n  -a: alpha value [defaults to 0.5]\n  -o: file to output json [defaults to ./mini.out.json]\n  -t: amount of time to run simulation [defaults to 100,000,000 iterations]\n```\n\n## Example\n\n```sh\nmake\n./bin/mini -n input/yeast.gw -N input/human.gw\n# or\n./bin/mini -n input/yeast.gw -N input/human.gw -s input/yeast_human.bitscores\n# or\n./bin/mini -n input/yeast.gw -N input/human.gw -s input/yeast_human.bitscores -a 0.995\n# or\n./bin/mini -n input/yeast.gw -N input/human.gw -a 0.995\n```\n\n## Planning\n\nCheck out our [kanban board](https://github.com/jamesalbert/minisana/projects/1)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjamesalbert%2Fminisana","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjamesalbert%2Fminisana","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjamesalbert%2Fminisana/lists"}