{"id":160806,"name":null,"description":"BIO index for genetic records stored in S3 and FastAPI server.","url":"https://github.com/broadinstitute/dig-bioindex","last_synced_at":"2025-09-09T18:13:24.572Z","repository":{"id":40739282,"uuid":"221059628","full_name":"broadinstitute/dig-bioindex","owner":"broadinstitute","description":"BIO index for genetic records stored in S3 and FastAPI server.","archived":false,"fork":false,"pushed_at":"2025-05-15T14:33:31.000Z","size":9537,"stargazers_count":6,"open_issues_count":3,"forks_count":6,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-09-05T04:39:07.789Z","etag":null,"topics":["ot2od036440"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/broadinstitute.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":"2019-11-11T19:59:39.000Z","updated_at":"2025-05-12T14:45:51.000Z","dependencies_parsed_at":"2023-09-28T20:58:14.351Z","dependency_job_id":"846d07ae-4588-4cfd-8c9d-fd068c3d7294","html_url":"https://github.com/broadinstitute/dig-bioindex","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/broadinstitute/dig-bioindex","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fdig-bioindex","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fdig-bioindex/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fdig-bioindex/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fdig-bioindex/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/broadinstitute","download_url":"https://codeload.github.com/broadinstitute/dig-bioindex/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fdig-bioindex/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274340541,"owners_count":25267294,"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":"2025-09-09T02:00:10.223Z","response_time":80,"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"}},"owner":{"login":"broadinstitute","name":"Broad Institute","uuid":"393552","kind":"organization","description":"Broad Institute of MIT and Harvard","email":null,"website":"http://www.broadinstitute.org/","location":"Cambridge, MA","twitter":"broadinstitute","company":null,"icon_url":"https://avatars.githubusercontent.com/u/393552?v=4","repositories_count":1083,"last_synced_at":"2023-04-09T09:48:11.262Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/broadinstitute","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-02T16:23:28.278Z","updated_at":"2023-04-09T09:48:11.836Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/broadinstitute","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/broadinstitute/repositories"},"packages":[],"commits":{"id":8085118,"full_name":"broadinstitute/dig-bioindex","default_branch":"master","committers":null,"total_commits":null,"total_committers":null,"total_bot_commits":null,"total_bot_committers":null,"mean_commits":null,"dds":null,"past_year_committers":null,"past_year_total_commits":null,"past_year_total_committers":null,"past_year_total_bot_commits":null,"past_year_total_bot_committers":null,"past_year_mean_commits":null,"past_year_dds":null,"last_synced_at":null,"last_synced_commit":null,"created_at":"2024-12-31T19:51:08.103Z","updated_at":"2024-12-31T19:51:08.103Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fdig-bioindex/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-09T00:17:06.873Z","repositories_count":5532314,"commits_count":870800544,"contributors_count":32076502,"owners_count":918195,"icon_url":"https://github.com/github.png","host_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories"}},"issues_stats":{"full_name":"broadinstitute/dig-bioindex","html_url":"https://github.com/broadinstitute/dig-bioindex","last_synced_at":"2024-12-31T20:14:15.662Z","status":null,"issues_count":0,"pull_requests_count":79,"avg_time_to_close_issue":null,"avg_time_to_close_pull_request":824649.28,"issues_closed_count":0,"pull_requests_closed_count":75,"pull_request_authors_count":7,"issue_authors_count":0,"avg_comments_per_issue":null,"avg_comments_per_pull_request":0.0759493670886076,"merged_pull_requests_count":66,"bot_issues_count":0,"bot_pull_requests_count":9,"past_year_issues_count":0,"past_year_pull_requests_count":27,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":585364.7391304348,"past_year_issues_closed_count":0,"past_year_pull_requests_closed_count":23,"past_year_pull_request_authors_count":4,"past_year_issue_authors_count":0,"past_year_avg_comments_per_issue":null,"past_year_avg_comments_per_pull_request":0.07407407407407407,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":6,"past_year_merged_pull_requests_count":19,"created_at":"2024-12-31T19:51:09.759Z","updated_at":"2025-09-02T19:09:51.534Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fdig-bioindex","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fdig-bioindex/issues","issue_labels_count":{"dependencies":1},"pull_request_labels_count":{"dependencies":8},"issue_author_associations_count":{"CONTRIBUTOR":1},"pull_request_author_associations_count":{"CONTRIBUTOR":59,"NONE":2,"MEMBER":1},"issue_authors":{"dependabot[bot]":1},"pull_request_authors":{"psmadbec":24,"sagehen03":18,"massung":8,"dependabot[bot]":8,"wnojopra":2,"qu-y":1,"ClintAtTheBroad":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-09T00:00:11.778Z","repositories_count":10196250,"issues_count":32245739,"pull_requests_count":101768105,"authors_count":10740850,"icon_url":"https://github.com/github.png","host_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories","owners_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/owners","authors_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors"},"past_year_issue_labels_count":{},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{},"past_year_pull_request_author_associations_count":{"CONTRIBUTOR":4,"NONE":2},"past_year_issue_authors":{},"past_year_pull_request_authors":{"psmadbec":4,"wnojopra":2},"maintainers":[{"login":"qu-y","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/qu-y"}],"active_maintainers":[]},"events":{"total":{"PushEvent":16,"PullRequestEvent":7,"ForkEvent":4,"CreateEvent":2},"last_year":{"PushEvent":16,"PullRequestEvent":7,"ForkEvent":4,"CreateEvent":2}},"keywords":["ot2od036440"],"dependencies":[{"ecosystem":"pypi","filepath":"requirements.txt","sha":null,"kind":"manifest","created_at":"2022-08-19T22:23:37.697Z","updated_at":"2022-08-19T22:23:37.697Z","repository_link":"https://github.com/broadinstitute/dig-bioindex/blob/master/requirements.txt","dependencies":[{"id":2094587572,"package_name":"aiofiles","ecosystem":"pypi","requirements":"==0.6","direct":true,"kind":"runtime","optional":false},{"id":2094587573,"package_name":"botocore","ecosystem":"pypi","requirements":"==1.20","direct":true,"kind":"runtime","optional":false},{"id":2094587574,"package_name":"boto3","ecosystem":"pypi","requirements":"==1.17","direct":true,"kind":"runtime","optional":false},{"id":2094587575,"package_name":"click","ecosystem":"pypi","requirements":"==7.0","direct":true,"kind":"runtime","optional":false},{"id":2094587576,"package_name":"fastapi","ecosystem":"pypi","requirements":"==0.65.2","direct":true,"kind":"runtime","optional":false},{"id":2094587577,"package_name":"graphene","ecosystem":"pypi","requirements":"==3.0","direct":true,"kind":"runtime","optional":false},{"id":2094587578,"package_name":"graphql-core","ecosystem":"pypi","requirements":"==3.1.2","direct":true,"kind":"runtime","optional":false},{"id":2094587579,"package_name":"orjson","ecosystem":"pypi","requirements":"==3.5","direct":true,"kind":"runtime","optional":false},{"id":2094587580,"package_name":"pydantic","ecosystem":"pypi","requirements":"==1.6.2","direct":true,"kind":"runtime","optional":false},{"id":2094587581,"package_name":"pymysql","ecosystem":"pypi","requirements":"==0.10","direct":true,"kind":"runtime","optional":false},{"id":2094587582,"package_name":"python-dotenv","ecosystem":"pypi","requirements":"==0.15","direct":true,"kind":"runtime","optional":false},{"id":2094587583,"package_name":"requests","ecosystem":"pypi","requirements":"==2.25","direct":true,"kind":"runtime","optional":false},{"id":2094587584,"package_name":"rich","ecosystem":"pypi","requirements":"==12.0","direct":true,"kind":"runtime","optional":false},{"id":2094587585,"package_name":"smart_open","ecosystem":"pypi","requirements":"==5.0","direct":true,"kind":"runtime","optional":false},{"id":2094587586,"package_name":"sqlalchemy","ecosystem":"pypi","requirements":"==1.4","direct":true,"kind":"runtime","optional":false},{"id":2094587587,"package_name":"typing-extensions","ecosystem":"pypi","requirements":"==4.1.1","direct":true,"kind":"runtime","optional":false},{"id":2094587588,"package_name":"uvicorn","ecosystem":"pypi","requirements":"==0.13","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"pypi","filepath":"setup.py","sha":null,"kind":"manifest","created_at":"2022-08-19T22:23:37.875Z","updated_at":"2022-08-19T22:23:37.875Z","repository_link":"https://github.com/broadinstitute/dig-bioindex/blob/master/setup.py","dependencies":[{"id":2094596650,"package_name":"aiofiles","ecosystem":"pypi","requirements":"\u003e=0.6","direct":true,"kind":"runtime","optional":false},{"id":2094596651,"package_name":"botocore","ecosystem":"pypi","requirements":"\u003e=1.20","direct":true,"kind":"runtime","optional":false},{"id":2094596652,"package_name":"boto3","ecosystem":"pypi","requirements":"\u003e=1.17","direct":true,"kind":"runtime","optional":false},{"id":2094596653,"package_name":"click","ecosystem":"pypi","requirements":"\u003e=7.0","direct":true,"kind":"runtime","optional":false},{"id":2094596654,"package_name":"fastapi","ecosystem":"pypi","requirements":"\u003e=0.60","direct":true,"kind":"runtime","optional":false},{"id":2094596655,"package_name":"graphql-core","ecosystem":"pypi","requirements":"\u003e=3.0","direct":true,"kind":"runtime","optional":false},{"id":2094596656,"package_name":"orjson","ecosystem":"pypi","requirements":"\u003e=3.5","direct":true,"kind":"runtime","optional":false},{"id":2094596657,"package_name":"pydantic","ecosystem":"pypi","requirements":"\u003e=1.4","direct":true,"kind":"runtime","optional":false},{"id":2094596658,"package_name":"pymysql","ecosystem":"pypi","requirements":"\u003e=0.10","direct":true,"kind":"runtime","optional":false},{"id":2094596659,"package_name":"python-dotenv","ecosystem":"pypi","requirements":"\u003e=0.15","direct":true,"kind":"runtime","optional":false},{"id":2094596660,"package_name":"requests","ecosystem":"pypi","requirements":"\u003e=2.25","direct":true,"kind":"runtime","optional":false},{"id":2094596661,"package_name":"rich","ecosystem":"pypi","requirements":"\u003e=10.0","direct":true,"kind":"runtime","optional":false},{"id":2094596662,"package_name":"smart_open","ecosystem":"pypi","requirements":"\u003e=5.0","direct":true,"kind":"runtime","optional":false},{"id":2094596663,"package_name":"sqlalchemy","ecosystem":"pypi","requirements":"\u003e=1.4","direct":true,"kind":"runtime","optional":false},{"id":2094596664,"package_name":"uvicorn","ecosystem":"pypi","requirements":"\u003e=0.13","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/codeql.yml","sha":null,"kind":"manifest","created_at":"2023-02-11T07:15:42.466Z","updated_at":"2023-02-11T07:15:42.466Z","repository_link":"https://github.com/broadinstitute/dig-bioindex/blob/master/.github/workflows/codeql.yml","dependencies":[{"id":7547090735,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":7547090736,"package_name":"github/codeql-action/init","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7547090737,"package_name":"github/codeql-action/autobuild","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7547090738,"package_name":"github/codeql-action/analyze","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"docker","filepath":"image/Dockerfile","sha":null,"kind":"manifest","created_at":"2023-02-11T07:15:42.487Z","updated_at":"2023-02-11T07:15:42.487Z","repository_link":"https://github.com/broadinstitute/dig-bioindex/blob/master/image/Dockerfile","dependencies":[{"id":7547090741,"package_name":"python","ecosystem":"docker","requirements":"3","direct":true,"kind":"build","optional":false}]},{"ecosystem":"docker","filepath":"batch-index-files/Dockerfile","sha":null,"kind":"manifest","created_at":"2023-09-28T20:58:13.820Z","updated_at":"2023-09-28T20:58:13.820Z","repository_link":"https://github.com/broadinstitute/dig-bioindex/blob/master/batch-index-files/Dockerfile","dependencies":[{"id":14003643260,"package_name":"ubuntu","ecosystem":"docker","requirements":"20.04","direct":true,"kind":"build","optional":false}]},{"ecosystem":"pypi","filepath":"batch-index-files/requirements.txt","sha":null,"kind":"manifest","created_at":"2023-09-28T20:58:14.036Z","updated_at":"2023-09-28T20:58:14.036Z","repository_link":"https://github.com/broadinstitute/dig-bioindex/blob/master/batch-index-files/requirements.txt","dependencies":[{"id":14003643263,"package_name":"boto3","ecosystem":"pypi","requirements":"==1.26.116","direct":true,"kind":"runtime","optional":false},{"id":14003643264,"package_name":"click","ecosystem":"pypi","requirements":"==8.1.3","direct":true,"kind":"runtime","optional":false},{"id":14003643265,"package_name":"bioindex","ecosystem":"pypi","requirements":"master","direct":true,"kind":"runtime","optional":false}]}],"score":null,"created_at":"2025-09-09T00:56:33.855Z","updated_at":"2025-10-07T08:38:27.526Z","avatar_url":"https://github.com/broadinstitute.png","language":"Python","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/160806","html_url":"https://science.ecosyste.ms/projects/160806"}