mims-harvard/tooluniverse

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tooluniverse-comparative-genomics Cross-species gene comparison and ortholog analysis.

mims-harvard/tooluniverse

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tooluniverse-population-genetics-1000genomes Population genetics using the 1000 Genomes Project (IGSR) — superpopulation/population search, sample metadata, varia…

mims-harvard/tooluniverse

216

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tooluniverse-electron-microscopy Search and analyze electron microscopy data — cryo-EM density maps (EMDB), fitted atomic models (PDB), raw micrograph…

mims-harvard/tooluniverse

215

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tooluniverse-kegg-disease-drug KEGG-based disease-drug-variant network research.

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215

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tooluniverse-lipidomics Lipid analysis and lipid-disease associations using LIPID MAPS classification, HMDB metabolite data, KEGG/Reactome li…

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tooluniverse-hla-immunogenomics HLA gene-family analysis and MHC-peptide binding for transplant compatibility, vaccine epitope coverage, and cancer i…

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tooluniverse-model-organism-genetics Cross-species genetic analysis using model organism databases (MGI mouse, ZFIN zebrafish, FlyBase fruit fly, WormBase…

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tooluniverse-computational-biophysics Solve quantitative problems in biophysics — pharmacokinetics (PK volume of distribution, clearance, half-life), epide…

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tooluniverse-variant-to-mechanism End-to-end variant-to-mechanism analysis — trace a variant (rsID/coordinates) through regulatory context, target gene…

mims-harvard/tooluniverse

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tooluniverse-acmg-variant-classification Systematic ACMG/AMP germline variant classification with all 28 criteria (PVS1, PS1-4, PM1-6, PP1-5, BA1, BS1-4, BP1-…

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tooluniverse-regulatory-variant-analysis Non-coding/regulatory variant interpretation — GWAS association lookup, eQTL evidence (GTEx), chromatin state (ENCODE…

mims-harvard/tooluniverse

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tooluniverse-cancer-classification Translate free-text tumor descriptions to OncoTree codes and resolve cancer subtypes/tissue hierarchy.

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tooluniverse-rare-disease-genomics Rare disease genomics — disease identification (Orphanet), causative gene discovery, gene-disease validity (GenCC), v…

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tooluniverse-vaccine-design Computational vaccine candidate design: peptide/subunit vaccines via MHC-I/MHC-II epitope prediction (IEDB), populati…

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tooluniverse-cell-line-profiling Cancer cell-line selection and profiling for experimental model choice.

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tooluniverse-variant-functional-annotation Functional annotation of protein variants — ProtVar structural/functional context, ClinVar clinical classifications, …

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tooluniverse-aging-senescence Aging biology, cellular senescence, and longevity research.

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tooluniverse-stem-cell-organoid Stem cell, iPSC, and organoid research — pluripotency markers, differentiation protocol pathways, lineage commitment …

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tooluniverse-functional-genomics-screens Interpret hits from CRISPR-KO/CRISPRi/shRNA screens by integrating DepMap essentiality, gnomAD constraint scores, pat…

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tooluniverse-noncoding-rna Non-coding RNA analysis — miRNAs (miRBase, miRDB targets), lncRNAs (LNCipedia, RNAcentral), circRNAs, snoRNAs, and ot…

mims-harvard/tooluniverse

203

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devtu-docs-quality TOP PRIORITY skill — find and immediately fix or remove every piece of wrong, outdated, or redundant information in T…

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170

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tooluniverse-microbiome-research Microbiome research using MGnify, GTDB, ENA, OLS (ENVO biomes), and EuropePMC.

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132

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tooluniverse-protein-interactions Protein-protein interaction (PPI) network analysis — STRING (predicted + experimental), BioGRID (curated), SASBDB (sm…

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tooluniverse-claude-code-plugin Install the ToolUniverse Claude Code plugin in one step — provides MCP server with 1000+ scientific tools, 120+ resea…

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tooluniverse-population-genetics Population genetics analysis — allele frequencies (gnomAD, 1000 Genomes), Hardy-Weinberg equilibrium testing, Fst bet…

mims-harvard/tooluniverse

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devtu-benchmark-harness Continuous improvement system for ToolUniverse tools, skills, and plugin. Run benchmarks, diagnose failures, route fi…

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tooluniverse-gene-regulatory-networks Gene regulatory network analysis — TF-target inference (JASPAR motifs, ChIP-seq), motif scanning, eQTL integration, p…

mims-harvard/tooluniverse

127

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tooluniverse-protein-structural-annotation-pdb Given a PDB structure, produce a per-residue annotation table: which residues sit at a binding interface (vs a partne…

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tooluniverse-protein-lof-mechanism Propose the mechanism by which a missense variant causes loss-of-function (LoF), synthesizing evidence from 5 indepen…

mims-harvard/tooluniverse

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tooluniverse-variant-predictor-dms-validation Validate a variant-effect predictor (AlphaMissense, ESM-C SAE, ESM logits, EVE, conservation scores, or any per-varia…

mims-harvard/tooluniverse

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tooluniverse-meta-analysis Meta-analysis / evidence synthesis — pool effect sizes across studies (odds ratios, risk ratios, hazard ratios, mean …

mims-harvard/tooluniverse

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tooluniverse-protein-sae-variant-interpretation Interpret a missense variant via ESMC-6B Sparse Autoencoder (SAE) feature activations. For a given protein + variant,…

mims-harvard/tooluniverse

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tooluniverse-residue-functional-mechanism-interpretation Given a set of residues in a protein, explain WHY they are functionally critical by combining structural context (bin…

mims-harvard/tooluniverse

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tooluniverse-mendelian-randomization Mendelian randomization (MR) causal inference — does an exposure, risk factor, or biomarker CAUSALLY affect a disease…

mims-harvard/tooluniverse

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tooluniverse-pharmacokinetics Pharmacokinetic (PK) analysis of concentration-time data — non-compartmental analysis (NCA) for Cmax, Tmax, AUC (0-t …

mims-harvard/tooluniverse

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tooluniverse-molecular-cloning Molecular cloning assembly design — Gibson Assembly (overlap design for seamless multi-fragment joining) and Golden G…

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tooluniverse-primer-design PCR / qPCR primer and oligo design — design forward/reverse primers for a target region (SantaLucia nearest-neighbor …

mims-harvard/tooluniverse

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tooluniverse-drug-synergy Drug-combination synergy analysis — quantify whether two drugs together are synergistic, additive, or antagonistic us…

mims-harvard/tooluniverse

107

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tooluniverse-diagnostic-test-evaluation Diagnostic test / biomarker accuracy — sensitivity, specificity, PPV, NPV, likelihood ratios, accuracy from a 2x2 tab…

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tooluniverse-dose-response Dose-response / concentration-response curve fitting — IC50, EC50, Hill slope, Emax/Emin efficacy, and relative poten…

mims-harvard/tooluniverse

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tooluniverse-enzyme-kinetics Enzyme kinetics — Michaelis-Menten Km, Vmax, kcat (turnover), and kcat/Km (catalytic efficiency / specificity constan…

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tooluniverse-clinical-risk-scoring Compute and interpret validated bedside clinical risk scores and pretest probabilities for an INDIVIDUAL patient — pi…

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tooluniverse-product-safety-surveillance >- Post-market safety surveillance and recall/adverse-event RETRIEVAL across the full spectrum of FDA-regulated produ…

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tooluniverse-codex-plugin Install, set up, verify, update, pin, uninstall, or troubleshoot the ToolUniverse plugin on OpenAI Codex. ALWAYS cons…

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tooluniverse-natural-product-dereplication Dereplicate a putative natural product and assign its chemical taxonomy. Use to answer "is [compound] a known natural…

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tooluniverse-microbial-genome-characterization Genome-ASSEMBLY discovery, QC, and replicon mapping for any organism (bacteria, archaea, fungi, and beyond) using NCB…

mims-harvard/tooluniverse

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tooluniverse-peptide-target-deorphanization Find the real protein target(s) of a peptide from its sequence — peptide target deorphanization / off-target identifi…

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Microbiome Research Analyze microbiome and metagenomics data using MGnify, GTDB, ENA, and literature tools. Search studies by biome/keywo…

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tooluniverse-self-review Review existing work against the user's actual goal and surface evidence-backed strengths, gaps, risks, and next fixe…

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tooluniverse-cs-setup Install or update ToolUniverse in Claude Science — create the conda env, install the tooluniverse pip package, and (r…

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