All Skills

Set up, launch, validate, and troubleshoot the USPTO downloader ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

Find commercial sources for chemical compounds — PubChem/ChEMBL identity resolution then vendor catalog search across ZINC, Enamine, eMolecules, Mcule. Compares pricing, availability, and identifies purchasable analogs when an exact compound is not in stock. Use for chemical procurement, virtual library curation, and 'where can I buy X' questions for synthesis planning.

Rare disease differential diagnosis from patient phenotype — HPO term matching to candidate diseases (Orphanet, OMIM), gene panel prioritization, ACMG variant interpretation, and structure-based variant analysis. Use for diagnostic odyssey assistance, phenotype-to-disease ranking, and genetic-counseling differential generation.

Population genetics using the 1000 Genomes Project (IGSR) — superpopulation/population search, sample metadata, variant frequencies across AFR/AMR/EAS/EUR/SAS, ancestry-specific analyses. Use for ancestry comparison, population-aware allele frequency lookups, and 1000-Genomes-cohort-specific analyses (distinct from gnomAD which has different sample composition).

Set up, launch, validate, and troubleshoot the Tangram ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

Set up, launch, validate, and troubleshoot the CellRank ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

Polygenic Risk Score (PRS) Builder

Immunology research workflows: antibody-antigen interactions, T/B cell repertoire, MHC/HLA binding prediction, autoimmune disease genetics, vaccine epitope mapping. Uses IEDB, IMGT, SAbDab, UniProt. Use for adaptive immunity questions, immune response analysis, antibody/TCR/BCR characterization, immunogenicity prediction, and immune-pathway-to-disease mapping.

Deep learning for single-cell omics using scvi-tools — probabilistic (VAE-based) batch correction and integration with scVI, semi-supervised integration and label transfer with scANVI, CITE-seq RNA+protein joint modeling with totalVI, scATAC-seq analysis with PeakVI, multiome RNA+ATAC joint modeling with MultiVI, spatial transcriptomics cell-type deconvolution with DestVI, and RNA velocity with veloVI. Use when scVI, scANVI, totalVI, PeakVI, MultiVI, DestVI, or veloVI are mentioned by name, or when a request needs deep-learning-based batch correction, reference mapping / scArches-style query-to-reference mapping, denoising single-cell counts, joint modeling of two modalities (RNA+protein, RNA+ATAC, single-cell+spatial), or a variational-autoencoder latent space for single-cell data — as opposed to classic scanpy/Harmony-based integration.

Gene-disease association analysis across DisGeNET, OpenTargets, Monarch, OMIM, GenCC, Orphanet, Gene2Phenotype (G2P). Cross-references multiple sources for evidence-graded association reports with concordance scoring (5/5 sources agree → strong, 1/5 → weak). Use for 'which diseases is gene X associated with' or 'which genes cause disease Y' queries with quantitative confidence, including clinical-panel-based curation (developmental disorders, cancer, cardiac, skeletal, eye, skin panels).

Set up, launch, validate, and troubleshoot the ColabDesign (BindCraft binder design) ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

End-to-end variant-to-mechanism analysis — trace a variant (rsID/coordinates) through regulatory context, target gene(s), molecular pathway(s), and phenotypic consequences. Integrates 7+ databases across 3 evidence layers (regulatory, molecular, disease) for a mechanistic model. Use for GWAS-hit-to-mechanism, eQTL-causal-gene tracing, and full causal-chain reports.

Gene-set enrichment analysis — GO (Biological Process, Molecular Function, Cellular Component), KEGG, Reactome pathway enrichment via clusterProfiler, gseapy, ORA, GSEA, plus g:Profiler for enrichment/ID conversion/ortholog mapping/SNP-to-gene annotation. Use for interpreting DEG lists, screen hit lists, or any gene-list-to-pathways query. Includes simplify-cutoff handling and union-vs-total denominator conventions for percent-DE questions.

Set up, launch, validate, and troubleshoot the ESM Cambrian ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

Analyze microbiome and metagenomics data using MGnify, GTDB, ENA, and literature tools. Search studies by biome/keyword, retrieve taxonomic profiles and functional annotations, classify genomes with GTDB taxonomy, and find related publications. Use for human gut microbiome, soil/ocean metagenomics, and environmental microbiology research.

Cancer cell-line selection and profiling for experimental model choice. Cross-references DepMap, Cellosaurus, COSMIC, PharmacoDB to deliver identity verification, mutation/CNV profile, gene dependencies, drug sensitivities, and druggable targets. Use to answer 'which cell line should I use for studying gene X?' or 'is this cell line a good model for cancer Y?'. Outputs ranked recommendations with rationale, growth characteristics, and known pitfalls.

Set up, launch, validate, and troubleshoot the ESMFold2-binder-design ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

De novo enzyme design by catalytic-motif scaffolding — build a transition-state motif, generate scaffolds with AlphaProtein Novo, fold every mechanistic state, and triage with mechanism-inspired filters (catalytic geometry, multi-state H-bonds, multi-resequence backbone scoring). Use for designing enzymes for a named reaction, scoring or filtering existing designs, or deciding which designs to order.

Therapeutic antibody engineering and optimization, lead-to-clinical-candidate. Covers sequence humanization (germline alignment, framework retention), affinity maturation, developability (aggregation, stability, PTMs), structure modeling (AlphaFold/PDB CDR analysis), immunogenicity prediction, and manufacturing feasibility. Use for biologic-drug optimization, mAb design review, biosimilar engineering, and clinical-precedent comparison.

Diagnostic test / biomarker accuracy — sensitivity, specificity, PPV, NPV, likelihood ratios, accuracy from a 2x2 table; ROC curve, AUC, and the optimal cutoff (Youden) for a continuous biomarker; and post-test probability via Bayes. Use when you have test results vs a gold standard (binary 2x2, or a continuous score + true labels) and need to judge how good the test is, pick a threshold, or compute the probability of disease given a result. Emphasizes the prevalence-dependence of PPV/NPV.

Computational vaccine candidate design: peptide/subunit vaccines via MHC-I/MHC-II epitope prediction (IEDB), population HLA coverage optimization, B-cell epitope identification, and cross-strain conservation analysis. Use for vaccine epitope prediction, HLA allele coverage, multi-epitope construct design, and immunogenicity assessment. Combines predicted MHC binding with experimentally validated IEDB epitopes for higher-confidence designs.

Set up, launch, validate, and troubleshoot the BioEmu-2 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

Search and retrieve clinical practice guidelines from 12+ authoritative sources — NICE, WHO, NCCN, AHA, ADA, SIGN, USPSTF, IDSA, NIH consensus, ESMO/ESC/EASL European societies, and US specialty associations. Use for evidence-graded treatment recommendations, dosing protocols, screening guidance, and authoritative-source-prioritized clinical guidance (NICE/WHO ranked above society guidelines).

Fix failing ToolUniverse tools by diagnosing test failures, identifying root causes, implementing fixes, and validating solutions. Use when ToolUniverse tools fail tests, return errors, have schema validation issues, or when asked to debug or fix tools in the ToolUniverse framework.