AIAgents4Pharma
AI Agents for drug discovery, drug development, and other pharmaceutical R&D
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- basico_model.py
- sys_bio_model.py
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- state_talk2biomodels.py
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- BIOMD0000000449_url.xml
- conftest.py
- test_api.py
- test_ask_question.py
- test_basico_model.py
- test_get_annotation.py
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- test_load_biomodel.py
- test_param_scan.py
- test_query_article.py
- test_save_model.py
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- 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
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- test_tools_param_sim_steady.py
- test_utils_and_loaders.py
- __init__.py
- ask_question.py
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- get_annotation.py
- get_modelinfo.py
- load_arguments.py
- load_biomodel.py
- parameter_scan.py
- query_article.py
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- __init__.py
- scp_agent.py
- __init__.py
- state_talk2cells.py
- test_scp_agent.py
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- README.md
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- t2kg_agent.py
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- biobridge_primekg.py
- dataset.py
- primekg.py
- starkqa_primekg.py
- .env.example
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- .env.example
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- __init__.py
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- adalimumab.md
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- DGE_human_Colon_UC-vs-Colon_Control.pdf
- DrugA.pdf
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- multimodal-analysis.csv
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- 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
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- test_tools_subgraph_summarization.py
- test_utils_database_milvus_connection_manager.py
- test_utils_embeddings_embeddings.py
- test_utils_embeddings_huggingface.py
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- test_utils_embeddings_ollama.py
- test_utils_embeddings_sentencetransformer.py
- test_utils_enrichments_enrichments.py
- test_utils_enrichments_ollama.py
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- test_utils_enrichments_pubchem.py
- test_utils_enrichments_reactome.py
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- test_utils_pubchem_utils.py
- __init__.py
- graphrag_reasoning.py
- load_arguments.py
- milvus_multimodal_subgraph_extraction.py
- multimodal_subgraph_extraction.py
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- subgraph_summarization.py
- __init__.py
- milvus_connection_manager.py
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- embeddings.py
- huggingface.py
- nim_molmim.py
- ollama.py
- sentence_transformer.py
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- enrichments.py
- ollama.py
- ols_terms.py
- pubchem_strings.py
- reactome_pathways.py
- uniprot_proteins.py
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- multimodal_pcst.py
- pcst.py
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- kg_utils.py
- pubchem_utils.py
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- 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
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- __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
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- 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
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- 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
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- install.md
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- prompt_general.txt
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- __init__.py
- streamlit_utils.py
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- 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
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- TESTING_LINTING.md
- WORKFLOWS.md
- Dwivedi_Model537_annotated.xml
- Dwivedi_Model537_empty.xml
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- example_models.md
- exp1.txt
- model537_mapping.xlsx
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- BIOMD0000000027_url.xml
- BIOMD0000000537_url.xml
- Tang2020.xml
- Task_Completion_set1.py
- task_completion_set1_results.json
- Task_Completion_set2.py
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- compartments_27.csv
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- scan_kdegIL6Gut_CRPExtacellular_537.csv
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- scan_MAPKK_Mpp_27.csv
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- scan_sigma_Hospitalized_971.csv
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- species_27.csv
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- units_27.pkl
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- benchmark.md
- benchmark_questions_set1.json
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- 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
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- tutorial_primekg_smiles_enrich_embed.ipynb
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- tutorial_starkqa_primekg_textual_enrichments.ipynb
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- tutorial.ipynb
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- Documentation_intro.md
- main_agent.md
- state_talk2aiagents4pharma.md
- intro.md
- t2b_agent.md
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- Case_1.md
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- 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
# Installation Guide
1. Get the code
git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
Downloads the entire project code from GitHub to your computer.
cd AIAgents4Pharma
Moves into the project folder you just downloaded.
2. Official Install Script
Easy RecommendedPrerequisites
- Python 3 Python is required to use pip.
pip install aiagents4pharma
Installs the package published on PyPI directly β no need to clone the source.
After installing, open a new terminal and run the program's version command (e.g. --version) to confirm it worked.
Pulled directly from this repo's README.
3. Docker
EasyPrerequisites
- Git Needed to download the project code from GitHub.
- Docker Desktop Needed to build and run containers. Install it and keep it running in the background.
β οΈ This is a large repository, so this method may point to an internal sub-package rather than the actual core product. Check the full README as well.
docker compose -f aiagents4pharma/talk2aiagents4pharma/docker-compose/cpu/docker-compose.yml up -d --build
Runs the command against the services defined in the compose file.
Run docker compose ps to check the containers are Up. If the README mentions a port, open http://localhost:PORT in your browser.
4. Python
EasyPrerequisites
pip install aiagents4pharma
Installs the package published on PyPI directly β no need to clone the source.
If it runs without errors and prints output in the terminal, it worked.
Pulled directly from this repo's README.
// repository documentation
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