{"id":170067,"name":null,"description":"TrialMatchAI aims to seamlessly match cancer patients to clinical trials based on their unique genomic and clinical profiles using AI","url":"https://github.com/cbib/trialmatchai","last_synced_at":"2025-09-09T21:19:27.778Z","repository":{"id":239617509,"uuid":"799899054","full_name":"cbib/TrialMatchAI","owner":"cbib","description":"TrialMatchAI aims to seamlessly match cancer patients to clinical trials based on their unique genomic and clinical profiles using AI","archived":false,"fork":false,"pushed_at":"2025-08-25T08:54:09.000Z","size":50960,"stargazers_count":14,"open_issues_count":0,"forks_count":1,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-08-25T11:01:49.364Z","etag":null,"topics":["artificial-intelligence","cancer-genomics","clinical-trials","large-language-models","personalized-medicine","personalized-recommendation","python"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cbib.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":"2024-05-13T10:13:40.000Z","updated_at":"2025-08-22T14:32:38.000Z","dependencies_parsed_at":"2025-08-25T10:24:34.280Z","dependency_job_id":"44adc9fe-762f-4b1b-a941-e4f08a2a8b49","html_url":"https://github.com/cbib/TrialMatchAI","commit_stats":null,"previous_names":["cbib/trialmatchai"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/cbib/TrialMatchAI","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbib%2FTrialMatchAI","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbib%2FTrialMatchAI/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbib%2FTrialMatchAI/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbib%2FTrialMatchAI/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cbib","download_url":"https://codeload.github.com/cbib/TrialMatchAI/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbib%2FTrialMatchAI/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274365928,"owners_count":25272293,"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":"cbib","name":"Centre de Bioinformatique de Bordeaux","uuid":"4851523","kind":"organization","description":"","email":null,"website":"https://www.cbib.u-bordeaux.fr/","location":"Université de Bordeaux (146, rue Léo Saignat 33076 Bordeaux cedex)","twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/4851523?v=4","repositories_count":15,"last_synced_at":"2024-03-27T07:12:18.804Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/cbib","funding_links":[],"total_stars":49,"followers":8,"following":0,"created_at":"2022-11-05T14:50:21.457Z","updated_at":"2024-03-27T07:12:20.679Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cbib","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cbib/repositories"},"packages":[],"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"cbib/TrialMatchAI","html_url":"https://github.com/cbib/TrialMatchAI","last_synced_at":null,"status":null,"issues_count":null,"pull_requests_count":null,"avg_time_to_close_issue":null,"avg_time_to_close_pull_request":null,"issues_closed_count":null,"pull_requests_closed_count":null,"pull_request_authors_count":null,"issue_authors_count":null,"avg_comments_per_issue":null,"avg_comments_per_pull_request":null,"merged_pull_requests_count":null,"bot_issues_count":null,"bot_pull_requests_count":null,"past_year_issues_count":null,"past_year_pull_requests_count":null,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":null,"past_year_issues_closed_count":null,"past_year_pull_requests_closed_count":null,"past_year_pull_request_authors_count":null,"past_year_issue_authors_count":null,"past_year_avg_comments_per_issue":null,"past_year_avg_comments_per_pull_request":null,"past_year_bot_issues_count":null,"past_year_bot_pull_requests_count":null,"past_year_merged_pull_requests_count":null,"created_at":"2025-08-31T06:58:26.995Z","updated_at":"2025-08-31T07:19:57.868Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbib%2FTrialMatchAI","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbib%2FTrialMatchAI/issues","issue_labels_count":{},"pull_request_labels_count":{},"issue_author_associations_count":{},"pull_request_author_associations_count":{"COLLABORATOR":2},"issue_authors":{},"pull_request_authors":{"mikageorges":2},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-09T00:00:11.778Z","repositories_count":10198121,"issues_count":32272968,"pull_requests_count":101825928,"authors_count":10741377,"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":{"COLLABORATOR":2},"past_year_issue_authors":{},"past_year_pull_request_authors":{"mikageorges":2},"maintainers":[{"login":"mikageorges","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/mikageorges"}],"active_maintainers":[{"login":"mikageorges","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/mikageorges"}]},"events":{"total":{"WatchEvent":10,"DeleteEvent":5,"MemberEvent":2,"PushEvent":23,"PullRequestEvent":2,"ForkEvent":1,"CreateEvent":3},"last_year":{"WatchEvent":10,"DeleteEvent":5,"MemberEvent":2,"PushEvent":23,"PullRequestEvent":2,"ForkEvent":1,"CreateEvent":3}},"keywords":["artificial-intelligence","cancer-genomics","clinical-trials","large-language-models","personalized-medicine","personalized-recommendation","python"],"dependencies":[{"ecosystem":"pypi","filepath":"requirements.txt","sha":null,"kind":"manifest","created_at":"2025-05-03T12:32:42.282Z","updated_at":"2025-05-03T12:32:42.282Z","repository_link":"https://github.com/cbib/TrialMatchAI/blob/main/requirements.txt","dependencies":[{"id":22965018217,"package_name":"bert_score","ecosystem":"pypi","requirements":"==0.3.13","direct":true,"kind":"runtime","optional":false},{"id":22965018218,"package_name":"bioregistry","ecosystem":"pypi","requirements":"==0.11.35","direct":true,"kind":"runtime","optional":false},{"id":22965018368,"package_name":"colorcet","ecosystem":"pypi","requirements":"==3.1.0","direct":true,"kind":"runtime","optional":false},{"id":22965018369,"package_name":"datasets","ecosystem":"pypi","requirements":"==2.19.0","direct":true,"kind":"runtime","optional":false},{"id":22965018370,"package_name":"elasticsearch","ecosystem":"pypi","requirements":"==9.0.0","direct":true,"kind":"runtime","optional":false},{"id":22965018371,"package_name":"faiss_cpu","ecosystem":"pypi","requirements":"==1.9.0.post1","direct":true,"kind":"runtime","optional":false},{"id":22965018372,"package_name":"falcon","ecosystem":"pypi","requirements":"==4.0.2","direct":true,"kind":"runtime","optional":false},{"id":22965018373,"package_name":"filelock","ecosystem":"pypi","requirements":"==3.18.0","direct":true,"kind":"runtime","optional":false},{"id":22965018374,"package_name":"FlagEmbedding","ecosystem":"pypi","requirements":"==1.3.3","direct":true,"kind":"runtime","optional":false},{"id":22965018754,"package_name":"FlagEmbedding","ecosystem":"pypi","requirements":"==1.3.4","direct":true,"kind":"runtime","optional":false},{"id":22965018755,"package_name":"gliner","ecosystem":"pypi","requirements":"==0.2.16","direct":true,"kind":"runtime","optional":false},{"id":22965018781,"package_name":"Jinja2","ecosystem":"pypi","requirements":"==3.1.6","direct":true,"kind":"runtime","optional":false},{"id":22965018782,"package_name":"joblib","ecosystem":"pypi","requirements":"==1.4.2","direct":true,"kind":"runtime","optional":false},{"id":22965018783,"package_name":"langchain","ecosystem":"pypi","requirements":"==0.3.23","direct":true,"kind":"runtime","optional":false},{"id":22965018784,"package_name":"langchain_community","ecosystem":"pypi","requirements":"==0.3.21","direct":true,"kind":"runtime","optional":false},{"id":22965018785,"package_name":"langchain_core","ecosystem":"pypi","requirements":"==0.3.52","direct":true,"kind":"runtime","optional":false},{"id":22965018786,"package_name":"langchain_openai","ecosystem":"pypi","requirements":"==0.3.13","direct":true,"kind":"runtime","optional":false},{"id":22965018787,"package_name":"local_gemma","ecosystem":"pypi","requirements":"==0.2.0","direct":true,"kind":"runtime","optional":false},{"id":22965018788,"package_name":"matplotlib","ecosystem":"pypi","requirements":"==3.10.1","direct":true,"kind":"runtime","optional":false},{"id":22965018789,"package_name":"nltk","ecosystem":"pypi","requirements":"==3.9.1","direct":true,"kind":"runtime","optional":false},{"id":22965018790,"package_name":"numpy","ecosystem":"pypi","requirements":"==2.2.4","direct":true,"kind":"runtime","optional":false},{"id":22965018791,"package_name":"openpyxl","ecosystem":"pypi","requirements":"==3.1.5","direct":true,"kind":"runtime","optional":false},{"id":22965018792,"package_name":"optimum","ecosystem":"pypi","requirements":"==1.23.3","direct":true,"kind":"runtime","optional":false},{"id":22965018793,"package_name":"pandas","ecosystem":"pypi","requirements":"==2.2.3","direct":true,"kind":"runtime","optional":false},{"id":22965018794,"package_name":"peft","ecosystem":"pypi","requirements":"==0.14.0","direct":true,"kind":"runtime","optional":false},{"id":22965018795,"package_name":"pycountry","ecosystem":"pypi","requirements":"==24.6.1","direct":true,"kind":"runtime","optional":false},{"id":22965018796,"package_name":"pydantic","ecosystem":"pypi","requirements":"==2.11.3","direct":true,"kind":"runtime","optional":false},{"id":22965018797,"package_name":"pymongo","ecosystem":"pypi","requirements":"==4.12.0","direct":true,"kind":"runtime","optional":false},{"id":22965018798,"package_name":"python-dotenv","ecosystem":"pypi","requirements":"==1.1.0","direct":true,"kind":"runtime","optional":false},{"id":22965018799,"package_name":"python_dateutil","ecosystem":"pypi","requirements":"==2.9.0.post0","direct":true,"kind":"runtime","optional":false},{"id":22965018800,"package_name":"rapidfuzz","ecosystem":"pypi","requirements":"==3.13.0","direct":true,"kind":"runtime","optional":false},{"id":22965018801,"package_name":"Requests","ecosystem":"pypi","requirements":"==2.32.3","direct":true,"kind":"runtime","optional":false},{"id":22965018802,"package_name":"rich","ecosystem":"pypi","requirements":"==14.0.0","direct":true,"kind":"runtime","optional":false},{"id":22965018803,"package_name":"scikit_learn","ecosystem":"pypi","requirements":"==1.6.1","direct":true,"kind":"runtime","optional":false},{"id":22965018804,"package_name":"scipy","ecosystem":"pypi","requirements":"==1.15.2","direct":true,"kind":"runtime","optional":false},{"id":22965018805,"package_name":"seaborn","ecosystem":"pypi","requirements":"==0.13.2","direct":true,"kind":"runtime","optional":false},{"id":22965018806,"package_name":"seqeval","ecosystem":"pypi","requirements":"==1.2.2","direct":true,"kind":"runtime","optional":false},{"id":22965018882,"package_name":"spacy","ecosystem":"pypi","requirements":"==3.7.5","direct":true,"kind":"runtime","optional":false},{"id":22965018883,"package_name":"statsmodels","ecosystem":"pypi","requirements":"==0.14.4","direct":true,"kind":"runtime","optional":false},{"id":22965018884,"package_name":"tenacity","ecosystem":"pypi","requirements":"==9.0.0","direct":true,"kind":"runtime","optional":false},{"id":22965018885,"package_name":"torch","ecosystem":"pypi","requirements":"==2.5.1","direct":true,"kind":"runtime","optional":false},{"id":22965018886,"package_name":"tqdm","ecosystem":"pypi","requirements":"==4.67.1","direct":true,"kind":"runtime","optional":false},{"id":22965018887,"package_name":"transformers","ecosystem":"pypi","requirements":"==4.49.0","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"docker","filepath":"elasticsearch/docker-compose.yml","sha":null,"kind":"manifest","created_at":"2025-08-25T10:24:31.547Z","updated_at":"2025-08-25T10:24:31.547Z","repository_link":"https://github.com/cbib/TrialMatchAI/blob/main/elasticsearch/docker-compose.yml","dependencies":[{"id":24831367543,"package_name":"docker.elastic.co/elasticsearch/elasticsearch","ecosystem":"docker","requirements":"${STACK_VERSION}","direct":true,"kind":"runtime","optional":false},{"id":24831367544,"package_name":"docker.elastic.co/kibana/kibana","ecosystem":"docker","requirements":"${STACK_VERSION}","direct":true,"kind":"runtime","optional":false}]}],"score":null,"created_at":"2025-09-09T01:24:44.686Z","updated_at":"2025-10-07T08:39:46.630Z","avatar_url":"https://github.com/cbib.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/170067","html_url":"https://science.ecosyste.ms/projects/170067"}