{"name":"io.github.mims-harvard/tooluniverse","slug":"mims-harvard-tooluniverse","title":null,"description":"2,500+ scientific tools for AI scientists: life science, research, literature, and more.","url":"https://mcp.market/server/mims-harvard-tooluniverse","rating":null,"grade":"C","score":69,"certified":false,"status":"active","category":"other","tags":[],"presence":{"score":68,"stars":1695,"forks":256,"downloads_week":6991,"last_push_at":"2026-09-19T16:00:23.000Z","license":"Apache-2.0"},"uptime":null,"claimed":false,"transport":"pypi","callable_via_gateway":false,"default_price_micros":0,"repository":"https://github.com/mims-harvard/ToolUniverse","website":"https://aiscientist.tools","version":"1.5.0","remotes":[],"packages":[{"registryType":"pypi","registryBaseUrl":"https://pypi.org","identifier":"tooluniverse","version":"1.5.0","runtimeHint":"uvx","transport":{"type":"stdio"},"packageArguments":[{"value":"tooluniverse-smcp-stdio","type":"positional"},{"description":"Compact mode enabled by default: only exposes 4 core tools (tool finder, tool executor, etc.) to prevent context window overflow. All 2,500+ tools remain accessible via the execute_tool function.","value":"--compact-mode","type":"positional"},{"description":"Specific tool categories to load (e.g., uniprot ChEMBL opentarget pubmed). Omit to load all tools. See full list: https://zitniklab.hms.harvard.edu/ToolUniverse/tools/tools_config_index.html","type":"named","name":"--categories","valueHint":"CATEGORY","isRepeated":true}],"environmentVariables":[{"description":"OpenAI API key for LLM-based tool finding and embedding features","isSecret":true,"name":"OPENAI_API_KEY"},{"description":"Anthropic API key for Claude-based features","isSecret":true,"name":"ANTHROPIC_API_KEY"},{"description":"Google Gemini API key for Gemini-based features","isSecret":true,"name":"GEMINI_API_KEY"},{"description":"OpenRouter API key for accessing 100+ LLM models","isSecret":true,"name":"OPENROUTER_API_KEY"},{"description":"Azure OpenAI API key (alternative to OpenAI)","isSecret":true,"name":"AZURE_OPENAI_API_KEY"},{"description":"HuggingFace token for accessing models and datasets","isSecret":true,"name":"HF_TOKEN"},{"description":"NCBI/PubMed API key for higher rate limits (10 req/sec vs 3 req/sec). Register at https://www.ncbi.nlm.nih.gov/account/","isSecret":true,"name":"NCBI_API_KEY"},{"description":"Semantic Scholar API key for higher rate limits (100 req/sec vs 1 req/sec). Register at https://www.semanticscholar.org/product/api","isSecret":true,"name":"SEMANTIC_SCHOLAR_API_KEY"},{"description":"BioGRID API key for protein-protein interaction queries. Register free at https://webservice.thebiogrid.org/","isSecret":true,"name":"BIOGRID_API_KEY"},{"description":"DisGeNET API key for gene-disease association data. Register free at https://www.disgenet.org/","isSecret":true,"name":"DISGENET_API_KEY"},{"description":"OMIM API key for Mendelian disease data. Register at https://omim.org/api","isSecret":true,"name":"OMIM_API_KEY"},{"description":"OncoKB API token for precision oncology annotations. Register at https://www.oncokb.org/apiAccess","isSecret":true,"name":"ONCOKB_API_TOKEN"},{"description":"NVIDIA NIM API key for AlphaFold2 structure prediction, molecular docking, and genomics tools. Get key at https://build.nvidia.com","isSecret":true,"name":"NVIDIA_API_KEY"},{"description":"USPTO API key for patent data access. Register at https://developer.uspto.gov/","isSecret":true,"name":"USPTO_API_KEY"},{"description":"UMLS API key for medical terminology and concept mapping. Register at https://uts.nlm.nih.gov/uts/","isSecret":true,"name":"UMLS_API_KEY"},{"description":"BRENDA enzyme database login email. Register at https://www.brenda-enzymes.org/","name":"BRENDA_EMAIL"},{"description":"BRENDA enzyme database login password","isSecret":true,"name":"BRENDA_PASSWORD"}]}],"tools":[{"name":"boltz2_docking","description":"Run the Boltz2 docking tool. Args: sequence: Protein sequence using single-letter amino acid codes. ligands: Ligand dictionaries with id and smiles fields. Returns dict: A dictionary containing the docking results with the following structure: - predicted_structure (str): The predicted protein-ligand complex structure in CIF format - structure_format (str): Format of the structure file (typically","write_action":true,"price_micros":0,"input_schema":null},{"name":"compute_depmap24q2_gene_correlations","description":"Run one bounded DepMap lookup without blocking the MCP event loop.","write_action":true,"price_micros":0,"input_schema":null},{"name":"find_tools","description":"Find and search available ToolUniverse tools using AI-powered search.","write_action":false,"price_micros":0,"input_schema":null},{"name":"get_abstract_from_patent_app_number","description":"Retrieve the abstract of a patent application by its application number. Args: applicationNumberText: An 8- to 16-digit USPTO application number. Returns dict: A dictionary containing the abstract text under the 'result' key or an error message under the 'error' key if the document could not be retrieved.","write_action":false,"price_micros":0,"input_schema":null},{"name":"get_claims_from_patent_app_number","description":"Retrieve the claims of a patent application by its application number. Args: applicationNumberText: An 8- to 16-digit USPTO application number. Returns dict: A dictionary containing the claims text under the 'result' key or an error message under the 'error' key if the document could not be retrieved.","write_action":false,"price_micros":0,"input_schema":null},{"name":"get_full_text_from_patent_app_number","description":"Retrieve the full text of a patent application by its application number. Args: applicationNumberText: An 8- to 16-digit USPTO application number. Returns dict: A dictionary containing the full text under the 'result' key or an error message under the 'error' key if the document could not be retrieved.","write_action":false,"price_micros":0,"input_schema":null},{"name":"run_compass_prediction","description":"Predict ICI response for one provider-rooted COMPASS TPM table.","write_action":true,"price_micros":0,"input_schema":null},{"name":"run_pinnacle_ppi_retrieval","description":"Retrieve embeddings without blocking the MCP event loop.","write_action":true,"price_micros":0,"input_schema":null},{"name":"run_transcriptformer_embedding_retrieval","description":"Retrieve embeddings without blocking the MCP event loop.","write_action":true,"price_micros":0,"input_schema":null},{"name":"search_tools","description":"","write_action":false,"price_micros":0,"input_schema":null}],"scan":{"score":69,"grade":"C","scanned_at":"2026-09-19T21:08:26.747Z","report":{"scannerVersion":"0.1.8","scannedAt":"2026-09-19T21:08:26.695Z","components":{"code":{"score":15,"max":25,"notes":["1500 source files scanned"]},"reliability":{"score":-1,"max":20,"notes":["no gateway calls yet and no remote to probe"]},"poisoning":{"score":-1,"max":15,"notes":["tools not inspected (local package is not executed); not counted"]},"auth":{"score":6,"max":15,"notes":["static API keys via environment variables"]},"maintenance":{"score":15,"max":15,"notes":["last push 0 days ago"]},"identity":{"score":9,"max":10,"notes":["registry namespace matches repository owner","GitHub account older than a year"]}},"findings":[{"id":"net.raw-ip","severity":"medium","component":"code","title":"Network call to a raw IP address","evidence":"tooluniverse-1.5.0/src/tooluniverse/cellmarker_tool.py: …_files/file/Cell_marker_All.xlsx\", \"http://117.50.127.228/CellMarker/CellMarker_download_files/fil…"},{"id":"exec.eval","severity":"medium","component":"code","title":"eval / new Function used","evidence":"tooluniverse-1.5.0/src/tooluniverse/cellpose_tool.py: …nt is needed. masks = model.eval(img, diameter=diameter, channels=channel…"}],"inputs":{"packages":[{"registryType":"pypi","identifier":"tooluniverse","version":"1.5.0","found":true,"dependencyCount":101,"publishedAt":"2026-09-16T22:08:17.751223Z","repositoryUrl":"https://github.com/mims-harvard/ToolUniverse"}],"repo":{"found":true,"owner":"mims-harvard","repo":"ToolUniverse","archived":false,"pushedAt":"2026-09-19T16:00:23Z","stars":1695,"forks":256,"openIssues":24,"ownerType":"Organization","ownerAvatarUrl":"https://avatars.githubusercontent.com/u/60720343?v=4","ownerCreatedAt":"2020-02-06T00:27:36Z","license":"Apache-2.0"},"icon":{"url":"https://avatars.githubusercontent.com/u/60720343?v=4&s=128","source":"registry","width":128,"height":128},"presence":{"stars":1695,"forks":256,"downloadsWeek":6991,"license":"Apache-2.0","lastPushAt":"2026-09-19T16:00:23.000Z","score":68}}}},"grade_history":[{"kind":"restore","fromGrade":"D","toGrade":"C","reason":"score 69: Network call to a raw IP address; eval / new Function used","createdAt":"2026-09-19T21:08:27.396Z"}],"reviews":[]}