{"id":24510914,"url":"https://github.com/virtualpatientengine/vpehackathonaiagentsco","last_synced_at":"2025-07-20T00:32:22.954Z","repository":{"id":259119584,"uuid":"865374292","full_name":"VirtualPatientEngine/VPEHackathonAIAgentsCO","owner":"VirtualPatientEngine","description":"Documentation, Notebooks, Code, and Data for the AI agents for life science hackathon in collaboration with CodeOcean and BioLabs","archived":false,"fork":false,"pushed_at":"2024-10-23T19:39:02.000Z","size":26086,"stargazers_count":0,"open_issues_count":3,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2024-10-24T06:30:13.254Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://virtualpatientengine.github.io/VPEHackathonAIAgentsCO","language":"Jupyter Notebook","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/VirtualPatientEngine.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":"2024-09-30T12:33:03.000Z","updated_at":"2024-10-23T19:38:39.000Z","dependencies_parsed_at":"2024-10-26T19:39:55.317Z","dependency_job_id":null,"html_url":"https://github.com/VirtualPatientEngine/VPEHackathonAIAgentsCO","commit_stats":null,"previous_names":["virtualpatientengine/vpehackathonaiagentsco"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/VirtualPatientEngine/VPEHackathonAIAgentsCO","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VirtualPatientEngine%2FVPEHackathonAIAgentsCO","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VirtualPatientEngine%2FVPEHackathonAIAgentsCO/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VirtualPatientEngine%2FVPEHackathonAIAgentsCO/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VirtualPatientEngine%2FVPEHackathonAIAgentsCO/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/VirtualPatientEngine","download_url":"https://codeload.github.com/VirtualPatientEngine/VPEHackathonAIAgentsCO/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VirtualPatientEngine%2FVPEHackathonAIAgentsCO/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266048559,"owners_count":23868741,"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","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":"2025-01-22T00:31:44.921Z","updated_at":"2025-07-20T00:32:17.932Z","avatar_url":"https://github.com/VirtualPatientEngine.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# VPE Hackathon: AI Agents for Life Sciences\nPlease visit the project page [website](https://virtualpatientengine.github.io/VPEHackathonAIAgentsCO/) for a detailed overview of the Hackathon tasks and results\n\n## ⚠️ Warning ⚠️\n- The results of the Hackathon are provided as with only minimal changes by the judges made during the evaluation and which were made to reproduce the participants final demos given at the end of the Hackathon.\n- The Hackathon code is currently specific to the Code Ocean capsule environment which was used to boost participant productivity and ensure reproducibility of results.\n- We are in the process of migrating the Talk2Biomodels code to a stand-alone repository following our internal code- and dev-ops to facilitate community engagement (be on the lookout 👀 for when we announce the completion of the migration).\n\n## Recommended environment setup options\n1. From a code ocean capsule\n2. From a Docker image locally or on the cloud\n3. From a python virtual environment\n\n## Running the projects\n### Assumed folder structure\n\u003e code/... # where the code lives\u003cbr\u003e\n\u003e data/... # where data assets live\u003cbr\u003e\n\u003e environment/... # where docker files and other environment setup scripts live\u003cbr\u003e\n\u003e results/... # where results are written to\u003cbr\u003e\n\n### From the command line\nRun the demo [README](./code/demo/README.md)\u003cbr\u003e\n`streamlit run /code/demo/streamlit_app.py`\u003cbr\u003e\nRun the Talk2Biomodels [README](./code/talk2biomodels/README.md)\u003cbr\u003e\n`streamlit run /code/talk2biomodels/streamlit_app.py`\u003cbr\u003e\nRun the Talk2Cells [README](./code/talk2cells/README.md)\u003cbr\u003e\n`streamlit run /code/talk2cells/streamlit_app.py`\u003cbr\u003e\nRun the Talk2KnowledgeGraphs [README](./code/talk2knowledgegraphs/README.md)\u003cbr\u003e\n`streamlit run /code/talk2knowledgegraphs/streamlit_app.py`\u003cbr\u003e\n\n### Caveats\n- Talk2Biomodels is currently not integrated with Ollama, and instead uses OpenAI which requires setting the environmental variable `OPENAI_API_KEY`\n- Demo, Talk2Cells, and Talk2KnowledgeGraphs require external data assets that were supplied during the Hackathon, which are explained in the [setup](https://virtualpatientengine.github.io/VPEHackathonAIAgentsCO/setup/) and project specific READMEs","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvirtualpatientengine%2Fvpehackathonaiagentsco","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvirtualpatientengine%2Fvpehackathonaiagentsco","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvirtualpatientengine%2Fvpehackathonaiagentsco/lists"}