AIAgents4Pharma
AI Agents for drug discovery, drug development, and other pharmaceutical R&D
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최종 버전 다운로드 (.zip)- bug_report.md
- config.yml
- documentation.md
- feature_request.md
- question.md
- docker_build.yml
- mkdocs_deploy.yml
- package_build.yml
- pr-automation.yml
- release.yml
- security_audit.yml
- sonarcloud.yml
- tests_talk2aiagents4pharma.yml
- tests_talk2biomodels.yml
- tests_talk2cells.yml
- tests_talk2knowledgegraphs.yml
- tests_talk2scholars.yml
- CODEOWNERS
- dependabot.yml
- labeler.yml
- PULL_REQUEST_TEMPLATE.md
- __init__.py
- main_agent.py
- default.yaml
- __init__.py
- __init__.py
- default.yaml
- __init__.py
- __init__.py
- config.yaml
- .env.example
- docker-compose.yml
- .env.example
- docker-compose.yml
- __init__.py
- state_talk2aiagents4pharma.py
- __init__.py
- test_main_agent.py
- .dockerignore
- __init__.py
- Dockerfile
- install.md
- README.md
- __init__.py
- t2b_agent.py
- __init__.py
- ols.py
- uniprot.py
- __init__.py
- default.yaml
- __init__.py
- __init__.py
- default.yaml
- __init__.py
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- default.yaml
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- default.yaml
- __init__.py
- default.yaml
- __init__.py
- __init__.py
- config.yaml
- __init__.py
- basico_model.py
- sys_bio_model.py
- __init__.py
- state_talk2biomodels.py
- __init__.py
- article_on_model_537.pdf
- BIOMD0000000449_url.xml
- conftest.py
- test_api.py
- test_ask_question.py
- test_basico_model.py
- test_get_annotation.py
- test_getmodelinfo.py
- test_integration.py
- test_load_biomodel.py
- test_param_scan.py
- test_query_article.py
- test_save_model.py
- test_search_models.py
- test_simulate_model.py
- test_state_and_agent.py
- test_steady_state.py
- test_sys_bio_model.py
- test_tools_annotation_and_modelinfo.py
- test_tools_ask_and_plot.py
- test_tools_branches_remaining.py
- test_tools_custom_plotter_extract.py
- test_tools_get_annotation_branches.py
- test_tools_get_annotation_branches_extra.py
- test_tools_get_modelinfo_errors.py
- test_tools_io.py
- test_tools_param_sim_steady.py
- test_utils_and_loaders.py
- __init__.py
- ask_question.py
- custom_plotter.py
- get_annotation.py
- get_modelinfo.py
- load_arguments.py
- load_biomodel.py
- parameter_scan.py
- query_article.py
- save_model.py
- search_models.py
- simulate_model.py
- steady_state.py
- utils.py
- .dockerignore
- __init__.py
- Dockerfile
- install.md
- README.md
- __init__.py
- scp_agent.py
- __init__.py
- state_talk2cells.py
- test_scp_agent.py
- __init__.py
- display_studies.py
- search_studies.py
- __init__.py
- __init__.py
- README.md
- __init__.py
- t2kg_agent.py
- __init__.py
- default.yaml
- __init__.py
- default.yaml
- __init__.py
- __init__.py
- default.yaml
- __init__.py
- default.yaml
- __init__.py
- default.yaml
- __init__.py
- default.yaml
- __init__.py
- __init__.py
- default.yaml
- default.yaml
- default.yaml
- default.yaml
- default.yaml
- __init__.py
- config.yaml
- __init__.py
- biobridge_primekg.py
- dataset.py
- primekg.py
- starkqa_primekg.py
- .env.example
- docker-compose.yml
- .env.example
- docker-compose.yml
- __init__.py
- state_talk2knowledgegraphs.py
- edges_0.parquet.gzip
- edges_1.parquet.gzip
- edges_10.parquet.gzip
- edges_11.parquet.gzip
- edges_2.parquet.gzip
- edges_3.parquet.gzip
- edges_4.parquet.gzip
- edges_5.parquet.gzip
- edges_6.parquet.gzip
- edges_7.parquet.gzip
- edges_8.parquet.gzip
- edges_9.parquet.gzip
- edges.parquet.gzip
- biological_process.parquet.gzip
- cellular_component.parquet.gzip
- disease.parquet.gzip
- drug.parquet.gzip
- gene_protein.parquet.gzip
- molecular_function.parquet.gzip
- biological_process.parquet.gzip
- cellular_component.parquet.gzip
- disease.parquet.gzip
- drug.parquet.gzip
- gene_protein.parquet.gzip
- molecular_function.parquet.gzip
- .~lock.multimodal-analysis.xlsx#
- adalimumab.md
- adalimumab.pdf
- biobridge_edges.parquet.gzip
- biobridge_multimodal_pyg_graph.pkl
- biobridge_multimodal_text_graph.pkl
- biobridge_nodes.parquet.gzip
- DGE_human_Colon_UC-vs-Colon_Control.pdf
- DrugA.pdf
- DrugB.pdf
- multimodal-analysis.csv
- multimodal-analysis.xlsx
- multimodal-analysis_sample_genes.xlsx
- multimodal-analysis_single_gene.xlsx
- primekg_ibd_pyg_graph.pkl
- primekg_ibd_text_graph.pkl
- __init__.py
- conftest.py
- test_agents_t2kg_agent.py
- test_datasets_biobridge_primekg.py
- test_datasets_dataset.py
- test_datasets_primekg.py
- test_datasets_starkqa_primekg.py
- test_state_talk2knowledgegraphs.py
- test_tools_graphrag_reasoning.py
- test_tools_milvus_multimodal_subgraph_extraction.py
- test_tools_multimodal_subgraph_extraction.py
- test_tools_subgraph_extraction.py
- test_tools_subgraph_summarization.py
- test_utils_database_milvus_connection_manager.py
- test_utils_embeddings_embeddings.py
- test_utils_embeddings_huggingface.py
- test_utils_embeddings_nim_molmim.py
- test_utils_embeddings_ollama.py
- test_utils_embeddings_sentencetransformer.py
- test_utils_enrichments_enrichments.py
- test_utils_enrichments_ollama.py
- test_utils_enrichments_ols.py
- test_utils_enrichments_pubchem.py
- test_utils_enrichments_reactome.py
- test_utils_enrichments_uniprot.py
- test_utils_extractions_milvus_multimodal_pcst.py
- test_utils_extractions_pcst.py
- test_utils_kg_utils.py
- test_utils_pubchem_utils.py
- __init__.py
- graphrag_reasoning.py
- load_arguments.py
- milvus_multimodal_subgraph_extraction.py
- multimodal_subgraph_extraction.py
- subgraph_extraction.py
- subgraph_summarization.py
- __init__.py
- milvus_connection_manager.py
- __init__.py
- embeddings.py
- huggingface.py
- nim_molmim.py
- ollama.py
- sentence_transformer.py
- __init__.py
- enrichments.py
- ollama.py
- ols_terms.py
- pubchem_strings.py
- reactome_pathways.py
- uniprot_proteins.py
- __init__.py
- milvus_multimodal_pcst.py
- multimodal_pcst.py
- pcst.py
- __init__.py
- kg_utils.py
- pubchem_utils.py
- .dockerignore
- __init__.py
- Dockerfile
- entrypoint.sh
- install.md
- milvus_data_dump.py
- README.md
- __init__.py
- main_agent.py
- paper_download_agent.py
- pdf_agent.py
- s2_agent.py
- zotero_agent.py
- __init__.py
- default.yaml
- __init__.py
- default.yaml
- __init__.py
- default.yaml
- __init__.py
- default.yaml
- __init__.py
- default.yaml
- __init__.py
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- __init__.py
- default.yaml
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- default.yaml
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- default.yaml
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- default.yaml
- __init__.py
- default.yaml
- __init__.py
- default.yaml
- __init__.py
- default.yaml
- __init__.py
- default.yaml
- __inti__.py
- default.yaml
- __init__.py
- __init__.py
- config.yaml
- .env.example
- docker-compose.yml
- .env.example
- docker-compose.yml
- __init__.py
- state_talk2scholars.py
- __init__.py
- test_agents_main_agent.py
- test_agents_paper_agents_download_agent.py
- test_agents_pdf_agent.py
- test_agents_s2_agent.py
- test_agents_zotero_agent.py
- test_s2_tools_display_dataframe.py
- test_s2_tools_query_dataframe.py
- test_states_state.py
- test_tools_paper_downloader.py
- test_tools_question_and_answer_tool.py
- test_tools_s2_multi.py
- test_tools_s2_retrieve.py
- test_tools_s2_search.py
- test_tools_s2_single.py
- test_utils_arxiv_downloader.py
- test_utils_base_paper_downloader.py
- test_utils_biorxiv_downloader.py
- test_utils_medrxiv_downloader.py
- test_utils_nvidia_nim_reranker.py
- test_utils_pdf_answer_formatter.py
- test_utils_pdf_batch_processor.py
- test_utils_pdf_collection_manager.py
- test_utils_pdf_document_processor.py
- test_utils_pdf_generate_answer.py
- test_utils_pdf_gpu_detection.py
- test_utils_pdf_paper_loader.py
- test_utils_pdf_rag_pipeline.py
- test_utils_pdf_retrieve_chunks.py
- test_utils_pdf_singleton_manager.py
- test_utils_pdf_vector_normalization.py
- test_utils_pdf_vector_store.py
- test_utils_pubmed_downloader.py
- test_utils_read_helper_utils.py
- test_utils_s2_utils_ext_ids.py
- test_utils_tool_helper_utils.py
- test_utils_zotero_human_in_the_loop.py
- test_utils_zotero_path.py
- test_utils_zotero_pdf_downloader_utils.py
- test_utils_zotero_read.py
- test_utils_zotero_write.py
- __init__.py
- arxiv_downloader.py
- base_paper_downloader.py
- biorxiv_downloader.py
- medrxiv_downloader.py
- pubmed_downloader.py
- __init__.py
- paper_downloader.py
- __init__.py
- answer_formatter.py
- batch_processor.py
- collection_manager.py
- document_processor.py
- generate_answer.py
- get_vectorstore.py
- gpu_detection.py
- nvidia_nim_reranker.py
- paper_loader.py
- rag_pipeline.py
- retrieve_chunks.py
- singleton_manager.py
- tool_helper.py
- vector_normalization.py
- vector_store.py
- __init__.py
- question_and_answer.py
- __init__.py
- multi_helper.py
- search_helper.py
- single_helper.py
- __init__.py
- display_dataframe.py
- multi_paper_rec.py
- query_dataframe.py
- retrieve_semantic_scholar_paper_id.py
- search.py
- single_paper_rec.py
- __init__.py
- read_helper.py
- review_helper.py
- write_helper.py
- zotero_path.py
- zotero_pdf_downloader.py
- __init__.py
- zotero_read.py
- zotero_review.py
- zotero_write.py
- __init__.py
- .dockerignore
- __init__.py
- Dockerfile
- install.md
- README.md
- __init__.py
- __init__.py
- prompt_ask_question.txt
- prompt_general.txt
- prompt_model_description.txt
- __init__.py
- streamlit_utils.py
- __init__.py
- streamlit_app.py
- streamlit_app_talk2aiagents4pharma.py
- streamlit_app_talk2biomodels.py
- streamlit_app_talk2cells.py
- streamlit_app_talk2knowledgegraphs.py
- streamlit_app_talk2scholars.py
- __init__.py
- AIAgents4Pharma.png
- t2agents_diagram.png
- t2b_diagram.png
- t2kg_diagram.png
- t2scholars_diagram.png
- VPE.png
- AZURE_DEPLOYMENT.md
- README.md
- SONARCLOUD_SETUP.md
- STREAMLIT_SECURITY.md
- TESTING_LINTING.md
- WORKFLOWS.md
- Dwivedi_Model537_annotated.xml
- Dwivedi_Model537_empty.xml
- Dwivedi_Model537_original.xml
- example_models.md
- exp1.txt
- model537_mapping.xlsx
- tutorial_load_model.ipynb
- tutorial_parameter_estimation.ipynb
- tutorial_sensitivity_analysis.ipynb
- BIOMD0000000027_url.xml
- BIOMD0000000537_url.xml
- Tang2020.xml
- Task_Completion_set1.py
- task_completion_set1_results.json
- Task_Completion_set2.py
- task_completion_set2_results.json
- compartments_27.csv
- compartments_537.csv
- compartments_971.csv
- parameters_27.csv
- parameters_537.csv
- parameters_971.csv
- scan_beta_Hospitalised_971.csv
- scan_beta_Infeceted_971.csv
- scan_Dose_CRP_537.csv
- scan_Exposed_Recovered_971.csv
- scan_IL6_CRP_537.csv
- scan_k1cat_M_27.csv
- scan_k1cat_Mpp_27.csv
- scan_k2cat_Mpp_27.csv
- scan_kdegIL6Gut_CRP_537.csv
- scan_kdegIL6Gut_CRPExtacellular_537.csv
- scan_kdegIL6Gut_IL6_537.csv
- scan_MAPKK_Mpp_27.csv
- scan_R_CRPExtracellular_537.csv
- scan_R_IL6_537.csv
- scan_sigma_Hospitalized_971.csv
- scan_sigma_Infected_971.csv
- species_27.csv
- species_537.csv
- species_971.csv
- stst_27.csv
- stst_971.csv
- tc_27.csv
- tc_537.csv
- tc_971.csv
- units_27.pkl
- units_537.pkl
- units_971.pkl
- benchmark.md
- benchmark_questions_set1.json
- benchmark_questions_set2.json
- benchmark_questions_set3.json
- benchmark_questions_set4.json
- expected_answers.ipynb
- generating_QnA_pairs.md
- tutorial_c2s.ipynb
- tutorial_cell_annotation.ipynb
- tutorial_cell_discovery.ipynb
- tutorial_cell_type_proportion.ipynb
- tutorial_UMAP_visualization.ipynb
- tutorial_biobridge_ibd_multimodal.ipynb
- tutorial_biobridge_multimodal.ipynb
- tutorial_biobridge_primekg_loader.ipynb
- tutorial_biobridge_primekg_protein_embeddings.ipynb
- tutorial_multimodal_embeddings_alignment.ipynb
- tutorial_primekg_enrichment.ipynb
- tutorial_primekg_loader.ipynb
- tutorial_primekg_milvus_data_dump.ipynb
- tutorial_primekg_milvus_ibd_primekg_dump.ipynb
- tutorial_primekg_smiles_enrich_embed.ipynb
- tutorial_primekg_subgraph.ipynb
- tutorial_pyg2dataframe.ipynb
- tutorial_starkqa_primekg_evaluation_vss.ipynb
- tutorial_starkqa_primekg_loader.ipynb
- tutorial_starkqa_primekg_textual_embeddings_all_minilm.ipynb
- tutorial_starkqa_primekg_textual_embeddings_nomic_embed_text.ipynb
- tutorial_starkqa_primekg_textual_enrichments.ipynb
- tutorial_talk2kg_agentic_tools.ipynb
- tutorial_uniprot_mapping.ipynb
- tutorial.ipynb
- CodeOps.md
- DevOps.md
- devops_1.jpg
- devops_10.png
- devops_11.png
- devops_2.png
- devops_3.png
- devops_4.png
- devops_5.jpg
- devops_6.png
- devops_7.png
- devops_8.png
- devops_9.png
- Documentation_intro.md
- main_agent.md
- state_talk2aiagents4pharma.md
- intro.md
- t2b_agent.md
- C1_q10.png
- C1_q11.png
- C1_q12.png
- C1_q14.png
- C1_q4.2.png
- C1_q4.3.png
- C1_q4.4.png
- C1_q5.png
- C1_q6.png
- C1_q8.png
- C2_q3.png
- C2_q4.png
- C3_q3.png
- C3_q6.png
- Case_1.md
- Case_2.md
- Case_3.md
- basico_model.md
- sys_bio_model.md
- state_talk2biomodels.md
- ask_question.md
- custom_plotter.md
- get_annotation.md
- get_modelinfo.md
- load_biomodel.md
- parameter_scan.md
- save_model.md
- search_models.md
- simulate_model.md
- steady_state.md
- faq.md
- intro.md
- intro.md
- scp_agent.md
- state_talk2cells.md
- display_studies.md
- search_studies.md
- intro.md
- t2kg_agent.md
- biobridge_primekg.md
- dataset.md
- primekg.md
- starkqa_primekg.md
- custom_data.md
- deployment.md
- state_talk2knowledgegraphs.md
- graphrag_reasoning.md
- load_arguments.md
- milvus_multimodal_subgraph_extraction.md
- multimodal_subgraph_extraction.md
- subgraph_extraction.md
- subgraph_summarization.md
- milvus_connection_manager.md
- embeddings.md
- huggingface.md
- nim_molmim.md
- ollama.md
- sentence_transformer.md
- enrichments.md
- ollama.md
- ols_terms.md
- pubchem_strings.md
- reactome_pathways.md
- uniprot_proteins.md
- milvus_multimodal_pcst.md
- multimodal_pcst.md
- pcst.md
- faq.md
- intro.md
- main_agent.md
- paper_download_agent.md
- pdf_agent.md
- s2_agent.md
- zotero_agent.md
- state_talk2scholars.md
- display_dataframe.md
- multi_paper_rec.md
- paper_downloader.md
- query_dataframe.md
- question_and_answer.md
- retrieve_semantic_scholar_paper_id.md
- search.md
- single_paper_rec.md
- zotero_read.md
- zotero_review.md
- zotero_write.md
- answer_formatter.md
- arxiv_downloader.md
- base_paper_downloader.md
- batch_processor.md
- biorxiv_downloader.md
- collection_manager.md
- document_processor.md
- generate_answer.md
- get_vectorstore.md
- gpu_detection.md
- medrxiv_downloader.md
- multi_helper.md
- nvidia_nim_reranker.md
- paper_loader.md
- pubmed_downloader.md
- rag_pipeline.md
- read_helper.md
- retrieve_chunks.md
- review_helper.md
- search_helper.md
- single_helper.md
- singleton_manager.md
- tool_helper.md
- vector_normalization.md
- vector_store.md
- write_helper.md
- zotero_path.md
- zotero_pdf_downloader.md
- intro.md
- CONTRIBUTING.md
- index.md
- robot.png
- t2b_diagram_latest.png
- .coveragerc
- .gitignore
- .pre-commit-config.yaml
- CHANGELOG.md
- CODE_OF_CONDUCT.md
- CONTRIBUTING.md
- LICENSE
- mkdocs.yml
- pyproject.toml
- README.md
- RELEASING.md
- SECURITY.md
- sonar-project.properties
- uv.lock
# 설치 가이드
1. 코드 내려받기
git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
깃허브에서 프로젝트 코드 전체를 내 컴퓨터로 내려받습니다.
cd AIAgents4Pharma
방금 내려받은 프로젝트 폴더 안으로 이동합니다.
2. 공식 설치 스크립트
쉬움 추천사전 준비물
- Python 3 pip 명령어를 쓰려면 Python이 필요합니다.
pip install aiagents4pharma
PyPI에 배포된 패키지를 바로 설치합니다. 소스 클론이 필요 없습니다.
설치 후 새 터미널을 열고, 프로그램의 버전 확인 명령(예: --version)으로 정상 설치됐는지 확인하세요.
이 레포의 README에 적힌 실제 명령어를 그대로 가져왔습니다.
3. Docker
쉬움사전 준비물
- Git GitHub에서 프로젝트 코드를 내려받으려면 필요합니다.
- Docker Desktop 컨테이너를 빌드하고 실행하려면 필요합니다. 설치 후 실행해서 백그라운드에 켜두세요.
⚠️ 이 프로젝트는 규모가 큰 저장소라, 이 방법이 실제 핵심 제품이 아니라 내부 하위 패키지를 가리키는 것일 수 있습니다. README 전체를 함께 확인해보세요.
docker compose -f aiagents4pharma/talk2aiagents4pharma/docker-compose/cpu/docker-compose.yml up -d --build
compose 설정 파일에 정의된 서비스들을 대상으로 명령을 실행합니다.
터미널에 docker compose ps 를 입력해 컨테이너들이 Up 상태인지 확인하세요. README에 포트 번호가 적혀있다면 브라우저에서 http://localhost:포트번호 로 접속해보세요.
// repository documentation
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