Artificial Intelligence for Medicine and Science at the Harvard Zitnik Lab publishes skills that let an AI agent work through biomedical research tasks, including finding RNA-seq and microarray gene expression datasets, scoring drug targets for druggability and safety, and analyzing chromatin accessibility and transcription factor binding from ENCODE and related sources. Their skills also cover small molecule lookup and procurement, diagnostic test accuracy calculations, and compound-target-disease network analysis for drug repurposing, along with setup guides for the Evo 2 and Squidpy remote tools in ToolUniverse.
Tooluniverse
392 skills · 1,775 stars · Apache-2.0
Create Tooluniverse Skill Create high-quality ToolUniverse skills following test-driven, implementation-agnostic methodology.
Devtu Benchmark Harness Continuous improvement system for ToolUniverse tools, skills, and plugin.
Devtu Remote Provider Bring up, standardise or debug a GPU-backed ToolUniverse remote tool in src/tooluniverse/remote/<…
Find gene expression RNA-seq and microarray datasets by tissue and condition Locate ArrayExpress and BioStudies omics datasets, rated for replicates and quality.
Host And Share Remote Tool Host, validate, and privately share a user's own model, Python function, workflow, or existing St…
Score drug targets for druggability, safety and go/no-go decisions A quantitative 0-100 target validation score with a GO/NO-GO recommendation.
Setup Af2Ig Remote Tool Set up, launch, validate, and troubleshoot the AlphaFold 2 initial-guess (dl_binder_design) ToolU…
Setup Af3_Jax Remote Tool Set up, launch, validate, and troubleshoot the AlphaFold 3 (JAX fork) ToolUniverse remote tool an…
Setup Af3_Torch Remote Tool Sets up, launches, validates, and troubleshoots the AF3-torch remote tool, an AlphaFold3 PyTorch re-
Setup Apnovo Remote Tool Set up, launch, validate, and troubleshoot the AlphaProtein Novo (de novo enzyme design) ToolUniv…
Setup Atlasfold Remote Tool Sets up, launches, validates, and troubleshoots the AtlasFold protein structure prediction ToolUnive
Setup Boltz Remote Tool Sets up and troubleshoots the Boltz-2 biomolecular affinity prediction model as a ToolUniverse remot
Setup Boltzgen Remote Tool Sets up, launches, validates, and troubleshoots the BoltzGen protein design model as a resident Tool
Setup Borzoi Remote Tool Sets up, launches, validates, and troubleshoots the Borzoi sequence-prediction model as a ToolUniver
Setup Borzoi_Calico Remote Tool Set up, launch, validate, and troubleshoot the calico/borzoi variant-scoring (SAD/logSAD/D2/logD2…
Setup Cell2Location Remote Tool Sets up, launches, validates, and troubleshoots the cell2location Python deconvolution model as a To
Setup Cellrank Remote Tool Sets up, validates, launches, and troubleshoots the CellRank fate-mapping model as a ToolUniverse MC
Setup Celltypist Remote Tool Sets up, runs, and troubleshoots the CellTypist cell-type annotation remote tool (run_celltypist_ann
Setup Chai1 Remote Tool Set up, launch, validate, and troubleshoot the Chai-1 ToolUniverse remote tool and optionally rel…
Setup Chrombpnet Remote Tool Sets up, launches, validates, and troubleshoots the ChromBPNet remote tool in ToolUniverse, a Python
Setup Colabdesign Remote Tool Set up, launch, validate, and troubleshoot the ColabDesign (BindCraft binder design) ToolUniverse…
Setup Colabfold Remote Tool Set up, launch, validate, and troubleshoot the ColabFold (AlphaFold2-Multimer) ToolUniverse remot…
Setup Complexa Remote Tool Set up, launch, validate, and troubleshoot the Proteina-Complexa ToolUniverse remote tool and opt…
Setup Depmap 24Q2 Remote Tool Sets up, runs, and troubleshoots the DepMap 24Q2 gene-correlation tool as a ToolUniverse MCP server 
Setup E1 Remote Tool Set up, launch, validate, and troubleshoot the Profluent E1 ToolUniverse remote tool and optional…
Setup Ef2Inv Remote Tool Set up, launch, validate, and troubleshoot the ESMFold2-binder-design ToolUniverse remote tool an…
Setup Enformer Remote Tool Sets up, launches, validates, and troubleshoots the Enformer genomic track-prediction model as a Too
Setup Enformer_Deepmind Remote Tool Set up, launch, validate, and troubleshoot the official DeepMind Enformer (TF-Hub SavedModel) gen…
Setup Esm Remote Tool Sets up, launches, validates, and troubleshoots the ESM protein language model (esm_embed_sequence) 
Setup Esm_If1 Remote Tool Set up, launch, validate, and troubleshoot the ESM-IF1 inverse-folding ToolUniverse remote tool a…
Setup Esmc Remote Tool Set up, launch, validate, and troubleshoot the ESM Cambrian ToolUniverse remote tool and optional…
Setup Esmfold2 Remote Tool Sets up, launches, validates, and troubleshoots the ESMFold2 protein structure folding remote tool i
Setup Evo2 Remote Tool Set up, launch, validate, and troubleshoot the Evo 2 ToolUniverse remote tool and optionally rela…
Setup Expert Feedback Remote Tool Set up, launch, validate, and troubleshoot the Human expert feedback ToolUniverse remote tool and…
Setup Genie3 Remote Tool Set up, launch, validate, and troubleshoot the Genie 3 ToolUniverse remote tool and optionally re…
Setup Gpnstar Remote Tool Set up, launch, validate, and troubleshoot the GPN-Star ToolUniverse remote tool (single-nucleoti…
Setup Harmony Remote Tool Sets up, launches, validates, and troubleshoots the Harmony ToolUniverse remote MCP tool (run_harmon
Setup Immune Compass Remote Tool Sets up, launches, validates, and troubleshoots the immune COMPASS remote tool, a CPU-run PyTorch ce
Setup Ldsc Remote Tool Sets up, launches, and verifies the LDSC (LD Score Regression) heritability and genetic-correlation 
Setup Liana Remote Tool Sets up and troubleshoots the LIANA cell-cell interaction remote tool for ToolUniverse, which expose
Setup Macs3 Remote Tool Sets up and troubleshoots the MACS3 peak-calling tool as a ToolUniverse remote MCP server, running i
Setup Milo Remote Tool Sets up, runs, validates, and troubleshoots the Milo differential abundance MCP server (run_milo_dif
Setup Mofa Remote Tool Sets up and troubleshoots the MOFA+ multi-omics factor analysis model as a ToolUniverse remote MCP t
Setup Monocle3 Remote Tool Set up, launch, validate, and troubleshoot the Monocle 3 ToolUniverse remote tool and optionally…
Setup Mosaic Remote Tool Set up, launch, validate, and troubleshoot the mosaic (Boltz-2 binder hallucination) ToolUniverse…
Setup Opendde Remote Tool Sets up, launches, validates and troubleshoots the OpenDDE all-atom co-folding model as a ToolUniver
Setup Openfold3 Remote Tool Sets up, launches, validates, and troubleshoots the OpenFold3 protein structure prediction remote to
Setup Openfold3_Ob0 Remote Tool Set up, launch, validate, and troubleshoot the OpenFold3 OpenBind-0 ToolUniverse remote tool and…