AI Agent Skills#
Specialized research workflows for ToolUniverse
ToolUniverse provides AI agent skills that teach agents how to conduct sophisticated scientific research. These skills combine multiple tools into expert-level workflows.
Important
Install all skills with one command:
npx skills add mims-harvard/ToolUniverse
Setup & Configuration#
Host, validate, and privately share a user’s own model, Python function, workflow, or existing Streamable HTTP MCP endpoint through ToolUniverse Pl…
Set up, launch, validate, and troubleshoot the Boltz-2 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when depl…
Set up, launch, validate, and troubleshoot the Borzoi ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deplo…
Set up, launch, validate, and troubleshoot the cell2location ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use whe…
Set up, launch, validate, and troubleshoot the CellRank ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when dep…
Set up, launch, validate, and troubleshoot the CellTypist ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when d…
Set up, launch, validate, and troubleshoot the ChromBPNet ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when d…
Set up, launch, validate, and troubleshoot the DepMap 24Q2 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when …
Set up, launch, validate, and troubleshoot the Enformer ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when dep…
Set up, launch, validate, and troubleshoot the ESM ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deployin…
Set up, launch, validate, and troubleshoot the Human expert feedback ToolUniverse remote tool and optionally relay it through ToolUniverse Connect….
Set up, launch, validate, and troubleshoot the Harmony ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when depl…
Set up, launch, validate, and troubleshoot the immune COMPASS ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use wh…
Set up, launch, validate, and troubleshoot the LDSC ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deployi…
Set up, launch, validate, and troubleshoot the LIANA ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploy…
Set up, launch, validate, and troubleshoot the MACS3 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploy…
Set up, launch, validate, and troubleshoot the Milo ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deployi…
Set up, launch, validate, and troubleshoot the MOFA+ ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploy…
Set up, launch, validate, and troubleshoot the Monocle 3 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when de…
Set up, launch, validate, and troubleshoot the PAGA ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deployi…
Set up, launch, validate, and troubleshoot the PINNACLE ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when dep…
Set up, launch, validate, and troubleshoot the scANVI ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deplo…
Set up, launch, validate, and troubleshoot the Scrublet ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when dep…
Set up, launch, validate, and troubleshoot the scVelo ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deplo…
Set up, launch, validate, and troubleshoot the scVI ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deployi…
Set up, launch, validate, and troubleshoot the SingleR ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when depl…
Set up, launch, validate, and troubleshoot the Slingshot ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when de…
Set up, launch, validate, and troubleshoot the Squidpy ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when depl…
Set up, launch, validate, and troubleshoot the Tangram ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when depl…
Install and configure ToolUniverse for any use case — MCP server (chat-based), CLI (command line with 9 subcommands), or Python SDK (Coding API wit…
Set up, launch, validate, and troubleshoot the TranscriptFormer ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use …
Set up, launch, validate, and troubleshoot the USPTO downloader ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use …
General Purpose#
“ToolUniverse plugin router. STEP 1 BEFORE ANY ANALYSIS: if the data folder contains *_executed.ipynb, run `tu run read_executed_notebook ‘{"dat…
Research Skills#
Create high-quality ToolUniverse skills following test-driven, implementation-agnostic methodology. disable-model-invocation: true
Systematic ACMG/AMP germline variant classification with all 28 criteria (PVS1, PS1-4, PM1-6, PP1-5, BA1, BS1-4, BP1-7) for clinical significance. …
Comprehensive ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) profiling for drug candidates. Integrates ADMET-AI predictions, Swi…
Detect and analyze adverse drug event signals using FDA FAERS reports, drug labels, and disproportionality statistics (PRR, ROR, IC). Generates qua…
Map environmental and industrial chemicals to adverse outcome pathways (AOPs) — molecular initiating event to organ-level toxicity. Uses AOPWiki, G…
Aging biology, cellular senescence, and longevity research. Covers senescence markers (p16/CDKN2A, SASP, SA-beta-gal), aging hallmarks, senolytic d…
Therapeutic antibody engineering and optimization, lead-to-clinical-candidate. Covers sequence humanization (germline alignment, framework retentio…
Install, set up, verify, update, pin, uninstall, or troubleshoot the ToolUniverse plugin on Google Antigravity (AGY / Antigravity IDE / Antigravity…
Discover novel small-molecule binders for protein targets using structure-based and ligand-based screening. Covers druggability assessment, known-l…
“Answer biomedical FACTUAL / recall / multiple-choice questions by querying ToolUniverse database tools instead of answering from memory. Triggers …
Translate free-text tumor descriptions to OncoTree codes and resolve cancer subtypes/tissue hierarchy. Cross-references UMLS/NCI vocabularies. Use …
TCGA/GDC cancer genomics analysis — cohort construction, clinical metadata retrieval, somatic mutation frequencies, survival analysis, and multi-om…
“Clinical interpretation of somatic cancer mutations for precision oncology. Transforms a gene + variant + cancer-type input into an actionable rep…
Cancer cell-line selection and profiling for experimental model choice. Cross-references DepMap, Cellosaurus, COSMIC, PharmacoDB to deliver identit…
Retrieve chemical compound data from PubChem and ChEMBL with disambiguation, cross-referencing, and stereochemistry handling. Use for resolving com…
Chemical safety and toxicology assessment integrating ADMET-AI predictions, CTD toxicogenomics, PubChemTox experimental data, GHS/IARC hazard class…
Find commercial sources for chemical compounds — PubChem/ChEMBL identity resolution then vendor catalog search across ZINC, Enamine, eMolecules, Mc…
Install the ToolUniverse Claude Code plugin in one step — provides MCP server with 1000+ scientific tools, 120+ research skills, slash commands, ho…
End-to-end drug safety review integrating FDA labels, FAERS adverse event reports, PRR/ROR disproportionality, pharmacogenomic biomarkers, clinical…
Search and retrieve clinical practice guidelines from 12+ authoritative sources — NICE, WHO, NCCN, AHA, ADA, SIGN, USPSTF, IDSA, NIH consensus, ESM…
Compute and interpret validated bedside clinical risk scores and pretest probabilities for an INDIVIDUAL patient — pick the right score for the sce…
Strategic clinical trial design feasibility assessment. Analyzes 6 dimensions (endpoint, population, comparator, effect size, duration, regulatory …
AI-driven patient-to-trial matching for precision oncology and rare-disease care. Transforms a patient’s molecular profile (mutations, biomarkers, …
Install, set up, verify, update, pin, uninstall, or troubleshoot the ToolUniverse plugin on OpenAI Codex. ALWAYS consult this skill for any of thos…
Cross-species gene comparison and ortholog analysis. Integrates Ensembl Compara orthologs, NCBI Gene, UniProt, OLS, Monarch, and OpenTargets to ide…
Solve quantitative problems in biophysics — pharmacokinetics (PK volume of distribution, clearance, half-life), epidemiology (R0, attack rate), tox…
Analyze CRISPR-Cas9 genetic screens — MAGeCK gene-level scores, sgRNA count QC, replicate correlation, hit prioritization, and pathway GSEA on scre…
Install or update ToolUniverse in Claude Science — create the conda env, install the tooluniverse pip package, and (re)build the tooluniverse-resea…
Add custom local tools to ToolUniverse alongside the 1000+ built-in tools. Covers JSON-config tools (simplest, no code), Python class tools (REST/S…
Integrate computed statistical results (DEGs, GWAS hits, associations) with biological context from ToolUniverse databases (UniProt, GO, Reactome, …
Universal data access patterns for downloading and parsing scientific data when ToolUniverse tools don’t cover the source, only return metadata, or…
Find and evaluate research datasets for any scientific question. Maps research questions to required study designs (longitudinal vs cross-sectional…
Diagnostic test / biomarker accuracy — sensitivity, specificity, PPV, NPV, likelihood ratios, accuracy from a 2x2 table; ROC curve, AUC, and the op…
Generate comprehensive disease research reports covering genetics (causal genes, GWAS, OMIM), pathways (Reactome, KEGG), drugs (existing therapies,…
Dose-response / concentration-response curve fitting — IC50, EC50, Hill slope, Emax/Emin efficacy, and relative potency from paired concentration v…
Assess drug-drug interactions — CYP metabolic interactions (substrate/inhibitor/inducer), transporter (P-gp, BCRP, OATP) effects, pharmacodynamic s…
Trace drug mechanism of action — primary target → downstream signaling → pathway perturbation → tissue/organ effect → clinical outcome. Uses DrugBa…
Drug regulatory and approval research — FDA substance registry, ATC/EPC classification, EMA decisions, generic-drug status, FDA Orange Book exclusi…
Identify drug repurposing candidates via target-based, compound-based, and disease-based strategies. Combines drug-target-disease network reasoning…
Comprehensive drug profiling — mechanism, primary/secondary targets, drug interactions, clinical-trial status, adverse events (FAERS), pharmacogeno…
Drug-combination synergy analysis — quantify whether two drugs together are synergistic, additive, or antagonistic using the standard reference mod…
Quantitative drug-target validation pipeline. Scores druggability, selectivity, safety profile, ADMET feasibility, and structural tractability with…
Ecology, biodiversity, and conservation biology research — species identification (GBIF, NCBI Taxonomy), invasive species impact, ecosystem dynamic…
Search and analyze electron microscopy data — cryo-EM density maps (EMDB), fitted atomic models (PDB), raw micrograph datasets (EMPIAR), and cryo-e…
Enzyme kinetics — Michaelis-Menten Km, Vmax, kcat (turnover), and kcat/Km (catalytic efficiency / specificity constant) from substrate-velocity dat…
End-to-end observational epidemiology analysis — from research question (PECO Population/Exposure/Comparator/Outcome) to publication-ready statisti…
“Genomics and epigenomics analysis: DNA methylation (CpG, 5mC, 5hmC, bisulfite, RRBS), m6A RNA modification (MeRIP-seq), ChIP-seq peaks, ATAC-seq a…
Histone-modification ChIP-seq, ATAC-seq accessibility, chromatin state, and TF binding analysis from ENCODE, Roadmap Epigenomics, ChIP-Atlas. Use f…
Retrieve gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation and quality assessment. Use for finding RNA-s…
FASTQ quality control and adapter/quality-trimming decisions with local NGS tools — run FastQC on raw reads, summarize a project with MultiQC, inte…
Interpret hits from CRISPR-KO/CRISPRi/shRNA screens by integrating DepMap essentiality, gnomAD constraint scores, pathway context (Reactome, STRING…
Gene-disease association analysis across DisGeNET, OpenTargets, Monarch, OMIM, GenCC, Orphanet. Cross-references multiple sources for evidence-grad…
Gene-set enrichment analysis — GO (Biological Process, Molecular Function, Cellular Component), KEGG, Reactome pathway enrichment via clusterProfil…
Evaluate the human safety liability of knocking down, knocking out, degrading, or pharmacologically inhibiting a gene. Use for gene safety scoring,…
Gene regulatory network analysis — TF-target inference (JASPAR motifs, ChIP-seq), motif scanning, eQTL integration, perturbation evidence (knockout…
GPCR receptor pharmacology — agonist/antagonist/inverse-agonist/biased-agonist classification, GPCRdb structural data, receptor-ligand binding anal…
Transform GWAS signals into drug targets and repurposing opportunities. Connects GWAS-significant loci to causal genes via fine-mapping/eQTL, then …
Statistical fine-mapping of GWAS loci using credible sets (SuSiE, FINEMAP) and locus-to-gene scoring (Open Targets L2G). Identifies likely causal v…
Interpret a single GWAS SNP across multiple databases — GWAS Catalog hits, LD/haplotype context, eQTL evidence, regulatory annotation, ClinVar path…
Compare GWAS studies, perform meta-analyses across cohorts, and assess signal replication. Uses GWAS Catalog metadata, study-level statistics, and …
Discover causal genes for diseases/traits from GWAS data using Open Targets L2G (locus-to-gene) scoring — integrates eQTL, chromatin interaction, a…
HLA gene-family analysis and MHC-peptide binding for transplant compatibility, vaccine epitope coverage, and cancer immunotherapy. Uses IMGT (HLA p…
Microscopy and quantitative imaging analysis — colony morphometry, fluorescence intensity quantification, cell-count statistics, dose-response curv…
TCR/BCR repertoire analysis — V(D)J segment usage, CDR3 sequence diversity, clonality scoring, antigen specificity matching to IEDB, public-clone i…
“Immunology research workflows: antibody-antigen interactions, T/B cell repertoire, MHC/HLA binding prediction, autoimmune disease genetics, vaccin…
Predict patient response to immune checkpoint inhibitors (ICIs) by integrating tumor mutational burden (TMB), microsatellite instability (MSI), PD-…
Rapid pathogen characterization and drug repurposing for outbreaks. Combines pathogen genomics (NCBI, BVBRC), host immune response (IEDB), drug-tar…
Inorganic chemistry, physical chemistry, and materials science — crystal structures, coordination chemistry, lattice parameters, thermodynamic prop…
Detect and auto-install missing ToolUniverse research skills. Checks common Claude Code/Cursor/Codex skill directories for the canary file, and ins…
KEGG-based disease-drug-variant network research. Connects diseases to causal genes, drugs to molecular targets, and variants to pathways using KEG…
Lipid analysis and lipid-disease associations using LIPID MAPS classification, HMDB metabolite data, KEGG/Reactome lipid pathways (sphingolipid, ei…
Deep literature review — PubMed, EuropePMC, bioRxiv preprints, citation networks, evidence synthesis. Disambiguates queries, runs collision-aware s…
Mendelian randomization (MR) causal inference — does an exposure, risk factor, or biomarker CAUSALLY affect a disease/outcome, using genetic varian…
Meta-analysis / evidence synthesis — pool effect sizes across studies (odds ratios, risk ratios, hazard ratios, mean differences, correlations, GWA…
Metabolomics research — metabolite identification, study analysis, and database searches across HMDB, MetaboLights, Metabolomics Workbench, KEGG. U…
Analyze metabolomics data end-to-end — metabolite identification, quantification (TIC normalization, batch correction), differential analysis, and …
Metabolomics pathway analysis — metabolite identification (HMDB, KEGG, ChEBI), pathway mapping (Reactome, KEGG, MetaCyc), disease associations, enz…
Microbiome and metagenomics analysis using MGnify, GTDB taxonomy, ENA sequencing data, and EuropePMC literature. Covers taxonomic classification, g…
Genome-ASSEMBLY discovery, QC, and replicon mapping for any organism (bacteria, archaea, fungi, and beyond) using NCBI Datasets. Resolves an organi…
Microbiome research using MGnify, GTDB, ENA, OLS (ENVO biomes), and EuropePMC. Covers study discovery, taxonomic profiling, host-microbe interactio…
Cross-species genetic analysis using model organism databases (MGI mouse, ZFIN zebrafish, FlyBase fruit fly, WormBase worm, SGD yeast, RGD rat, GBI…
Molecular cloning, in both directions. DESIGN — Gibson Assembly (overlap design for seamless multi-fragment joining) and Golden Gate Assembly (Type…
Multi-omics integration — orchestrate per-layer analysis (transcriptomics, proteomics, epigenomics, genomics, metabolomics) then perform cross-omic…
Comprehensive disease characterization across genomics, transcriptomics, proteomics, and pathways for systems-level understanding. Identifies thera…
Dereplicate a putative natural product and assign its chemical taxonomy. Use to answer “is [compound] a known natural product”, “what microbe/organ…
Compound-target-disease network construction and analysis for drug repurposing, polypharmacology discovery, and multi-target drug design. Uses STRI…
“Neuroscience research workflows: neuroanatomy, neural circuits, neurotransmitter biology, neurological/psychiatric disease genetics, neural-protei…
Non-coding RNA analysis — miRNAs (miRBase, miRDB targets), lncRNAs (LNCipedia, RNAcentral), circRNAs, snoRNAs, and other ncRNA classes. Distinct me…
Organic chemistry reasoning guide for reaction product prediction, mechanism analysis (electrophilic/nucleophilic substitution, addition, eliminati…
Connect GWAS variants to biological pathways and druggable targets. Maps GWAS hits to causal genes (via fine-mapping/eQTL), then to pathways (React…
Find the real protein target(s) of a peptide from its sequence — peptide target deorphanization / off-target identification, for ANY target class (…
Pharmacogenomics (PGx) research — drug-gene interactions (CPIC, PharmGKB), CPIC dosing guidelines, variant-drug-response associations, ethnic-allel…
Pharmacokinetic (PK) analysis of concentration-time data — non-compartmental analysis (NCA) for Cmax, Tmax, AUC (0-t and 0-∞), terminal half-life, …
Drug safety and adverse event analysis — FAERS spontaneous-report mining, FDA black-box warnings, signal detection (PRR, ROR, IC), risk factors by …
Cross-ancestry / cross-biobank phenome-wide association (PheWAS) and replication. Given ONE variant (rsID) or ONE gene, look up every phenotype it …
Phylogenetic analysis — de novo multiple sequence alignment (Clustal Omega/MUSCLE/MAFFT via EBI_msa_align) and neighbour-joining/UPGMA tree buildin…
Plant genomics and biology research — PlantReactome pathways, Ensembl Plants gene structure, POWO species taxonomy, UniProt annotation, KEGG plant …
Build and interpret polygenic risk scores (PRS) for complex diseases using GWAS summary statistics. Covers PRS construction (clumping/thresholding,…
Population genetics analysis — allele frequencies (gnomAD, 1000 Genomes), Hardy-Weinberg equilibrium testing, Fst between populations, GWAS associa…
Population genetics using the 1000 Genomes Project (IGSR) — superpopulation/population search, sample metadata, variant frequencies across AFR/AMR/…
Patient stratification for precision medicine — integrate genomic, clinical, and therapeutic data to split patients into responder/non-responder gr…
Cancer treatment recommendations from molecular profile (mutations + cancer type + biomarkers) — FDA-approved + investigational therapies, resistan…
PCR / qPCR primer and oligo design — design forward/reverse primers for a target region (SantaLucia nearest-neighbor thermodynamics), compute melti…
>- Post-market safety surveillance and recall/adverse-event RETRIEVAL across the full spectrum of FDA-regulated products that are NOT covered by th…
Protein-protein interaction (PPI) network analysis — STRING (predicted + experimental), BioGRID (curated), SASBDB (small-angle scattering). Disting…
“Propose the mechanism by which a missense variant causes loss-of-function (LoF), synthesizing evidence from 5 independent layers: AlphaMissense pa…
Post-translational modification (PTM) analysis — phosphorylation, ubiquitination, acetylation, glycosylation, methylation. Uses iPTMnet (sites + en…
“Interpret a missense variant via ESMC-6B Sparse Autoencoder (SAE) feature activations. For a given protein + variant, computes which interpretable…
“Given a PDB structure, produce a per-residue annotation table: which residues sit at a binding interface (vs a partner chain), which line a ligand…
Protein 3D structure prediction from sequence — ESMFold de novo prediction, AlphaFold database retrieval, experimental structures from RCSB, ProtVa…
Protein structure retrieval from RCSB PDB, PDBe, and AlphaFold with disambiguation, quality assessment (resolution, R-factor, pLDDT), and metadata….
AI-guided de novo protein design — RFdiffusion backbone generation, ProteinMPNN sequence design, structure validation (pLDDT, pTM, MPNN scores). Us…
Mass-spec proteomics analysis — protein identification, quantification (LFQ, TMT, iTRAQ), differential expression (tumor vs normal, treatment vs co…
Find and retrieve proteomics datasets from MassIVE and ProteomeXchange. Search by species, keyword, or accession; retrieve detailed metadata (instr…
Rare disease differential diagnosis from patient phenotype — HPO term matching to candidate diseases (Orphanet, OMIM), gene panel prioritization, A…
Rare disease genomics — disease identification (Orphanet), causative gene discovery, gene-disease validity (GenCC), variant interpretation (ClinVar…
Transcription factor binding, cis-regulatory elements (cCREs), chromatin accessibility, and regulatory annotation using JASPAR (motifs), ENCODE (cC…
Non-coding/regulatory variant interpretation — GWAS association lookup, eQTL evidence (GTEx), chromatin state (ENCODE), regulatory variant scoring …
“Given a set of residues in a protein, explain WHY they are functionally critical by combining structural context (binding interface, ligand pocket…
RNA-seq differential expression analysis with DESeq2, edgeR, and limma-voom — DEG lists, fold changes, dispersion estimation, design formulas inclu…
Build AI scientist systems with the ToolUniverse Python SDK for scientific research. Covers the 3 calling patterns (tu.run portable dict API, `tu…
> Review existing work against the user’s actual goal and surface evidence-backed strengths, gaps, risks, and next fixes. Use when asked to eval, e…
Biological sequence analysis — gene/protein sequence retrieval (NCBI, Ensembl, UniProt), nucleotide/protein search, ortholog discovery, and FASTQ Q…
Single-cell RNA-seq analysis with scanpy/anndata — h5ad data loading, scRNA-seq quality control and QC gating (n_genes_by_counts, total_counts, mit…
Small molecule identification, characterization, and procurement — PubChem, ChEMBL, BindingDB, ADMET-AI, SwissADME, eMolecules, Enamine. Covers com…
Spatial multi-omics interpretation pipeline. Transforms spatially variable genes (SVGs), domain annotations, and tissue context into biological ins…
Spatial transcriptomics analysis — Visium, MERFISH, seqFISH, Slide-seq. Maps gene expression to tissue architecture, identifies spatially variable …
Statistical modeling — linear/logistic/ordinal/Poisson regression, ANOVA, Kruskal-Wallis, chi-square, Mann-Whitney, Cox survival, spline fits (R `n…
Stem cell, iPSC, and organoid research — pluripotency markers, differentiation protocol pathways, lineage commitment factors, organoid model select…
Structural biology plus proteomics integration for drug target validation. Combines PDB experimental structures, AlphaFold predictions, GPCRdb, SAb…
“Structural variant (SV) clinical interpretation: deletions, duplications, inversions, translocations, complex rearrangements. Applies ACMG-adapted…
Systems biology and pathway analysis integrating Reactome, KEGG, WikiPathways, BioCarta, NCI-Nature Pathway Interaction Database. Multi-database pa…
Comprehensive drug-target intelligence — tissue expression (GTEx, HPA), pathways, protein interactions (STRING), variant landscape (ClinVar, gnomAD…
Drug and chemical toxicity assessment via adverse outcome pathways (AOPs), real-world FAERS adverse event signals, FDA labels, and toxicogenomic as…
“Computational vaccine candidate design: peptide/subunit vaccines via MHC-I/MHC-II epitope prediction (IEDB), population HLA coverage optimization,…
VCF and variant analysis — parsing, annotation, classification (synonymous, missense, frameshift, stop_gained), VAF filtering, coding vs non-coding…
Functional annotation of protein variants — ProtVar structural/functional context, ClinVar clinical classifications, gnomAD population frequencies,…
Clinical variant interpretation from raw variant calls to ACMG-classified recommendations with structural impact analysis. Use for VUS classificati…
“Validate a variant-effect predictor (AlphaMissense, ESM-C SAE, ESM logits, EVE, conservation scores, or any per-variant numeric score) against exp…
End-to-end variant-to-mechanism analysis — trace a variant (rsID/coordinates) through regulatory context, target gene(s), molecular pathway(s), and…
Development Skills#
Automatically discover life science APIs online, create ToolUniverse tools, validate them, and prepare integration PRs. Performs gap analysis to id…
“Continuous improvement system for ToolUniverse tools, skills, and plugin. Run benchmarks, diagnose failures, route fixes to devtu skills, retest. …
> Code quality patterns and guidelines for ToolUniverse tool development. Apply when writing, fixing, or refactoring tool Python code in the ToolUn…
Create new scientific tools for ToolUniverse framework with proper structure, validation, and testing. Use when users need to add tools to ToolUniv…
“TOP PRIORITY skill — find and immediately fix or remove every piece of wrong, outdated, or redundant information in ToolUniverse docs. Wrong code,…
Fix failing ToolUniverse tools by diagnosing test failures, identifying root causes, implementing fixes, and validating solutions. Use when ToolUni…
GitHub workflow for ToolUniverse - push code safely by moving temp files, activating pre-commit hooks, running tests, and cleaning staged files. Us…
Optimize tool descriptions in ToolUniverse JSON configs for clarity and usability. Reviews descriptions for missing prerequisites, unexpanded abbre…
Optimize ToolUniverse skills for better report quality, evidence handling, and user experience. Apply patterns like tool verification, foundation d…
> Orchestrate the full ToolUniverse self-improvement cycle: discover APIs, create tools, test with researcher personas, fix issues, optimize skills…
How to Use Skills#
After installation, skills are available in your AI coding agent. Some agents activate skills automatically based on your questions, while others may require you to explicitly mention the skill name.
Ask: “Research aspirin comprehensively”
Activates: tooluniverse-drug-research
Ask: “Analyze EGFR as a drug target”
Activates: tooluniverse-target-research
Ask: “Generate disease report for diabetes”
Activates: tooluniverse-disease-research
Ask: “Deep literature review on CRISPR”
Activates: tooluniverse-literature-deep-research