All Skills

Set up, launch, validate, and troubleshoot the Boltz-2 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.

Analyze CRISPR-Cas9 genetic screens — MAGeCK gene-level scores, sgRNA count QC, replicate correlation, hit prioritization, and pathway GSEA on screen output. Use for genome-wide essentiality screens, synthetic-lethality discovery, dropout vs positive-selection screen analysis, target identification, and resistance-screen interpretation. Includes screen-QC and statistical thresholds.

Stem cell, iPSC, and organoid research — pluripotency markers, differentiation protocol pathways, lineage commitment factors, organoid model selection. Use for iPSC characterization, differentiation protocol design via developmental-pathway recapitulation, and organoid-model selection for disease modeling.

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

Drug safety and adverse event analysis — FAERS spontaneous-report mining, FDA black-box warnings, signal detection (PRR, ROR, IC), risk factors by demographic/comorbidity, label change tracking, and SIDER curated label-derived side-effect frequencies. Use for post-market safety surveillance, AE signal investigation, drug-AE association strength scoring, "what side effects does drug X have" questions, and pharmacovigilance reports.

Mass-spec proteomics analysis — protein identification, quantification (LFQ, TMT, iTRAQ), differential expression (tumor vs normal, treatment vs control), PTM identification, and pathway enrichment on protein lists. Use when you have proteomics MS output, asking about protein abundance differences, or doing systems-level proteomic interpretation.

Analyze protein-protein interaction networks using STRING, BioGRID, and SASBDB databases. Maps protein identifiers, retrieves interaction networks with confidence scores, performs functional enrichment analysis (GO/KEGG/Reactome), and optionally includes structural data. No API key required for core functionality (STRING). Use when analyzing protein networks, discovering interaction partners, identifying functional modules, or studying protein complexes.

Clinical interpretation of somatic cancer mutations for precision oncology. Transforms a gene + variant + cancer-type input into an actionable report: clinical evidence tier (CIViC, OncoKB), therapeutic options (FDA-approved + investigational), resistance mechanisms, prognosis, and matching clinical trials. Use for tumor-board variant calls, somatic-mutation actionability assessment, and treatment selection. Always cancer-type-specific.

Pharmacogenomics (PGx) research — drug-gene interactions (CPIC, PharmGKB), CPIC dosing guidelines, variant-drug-response associations, ethnic-allele-frequency considerations, and metabolizer-status scoring. Use for PGx-informed dosing recommendations, CYP/HLA pharmacogenomic allele interpretation, and clinically-actionable PGx report generation.

Integrate computed statistical results (DEGs, GWAS hits, associations) with biological context from ToolUniverse databases (UniProt, GO, Reactome, ClinVar, OpenTargets). Use for adding gene function/pathway/disease annotations to a result list, building biological narrative around statistical findings, and going beyond p-values to mechanism.

Web Performance Detective

Drug regulatory and approval research — FDA substance registry, ATC/EPC classification, EMA decisions, generic-drug status, FDA Orange Book exclusivity, NDA/BLA pathways. Use for jurisdiction-aware approval status (FDA vs EMA), generic vs brand availability, exclusivity expiry tracking, and regulatory pathway selection. Always specifies the market when reporting status.

RNA-seq differential expression analysis with DESeq2, edgeR, and limma-voom — DEG lists, fold changes, dispersion estimation, design formulas including covariates, multi-condition contrasts, and Venn-set operations across groups. Routes across DESeq2 (default), edgeR (QL-F / exact test for small replicate counts), and limma-voom (large n / complex designs). Use when you have a count matrix + metadata, want to find DEGs, or need dispersion/PCA/clustering analysis. Includes RULE ZERO precedence (read executed.ipynb if present).

Single-cell RNA-seq analysis with scanpy/anndata — h5ad data loading, scRNA-seq quality control and QC gating (n_genes_by_counts, total_counts, mitochondrial percent / pct_counts_mt, pct_counts_ribo, doublet detection with Scrublet/scDblFinder, ambient RNA / SoupX awareness, empty-droplet filtering, MAD-based thresholds), normalization, dimensionality reduction (PCA, UMAP, t-SNE), clustering (Leiden, Louvain), marker gene identification, cell-type annotation, pseudotime/trajectory analysis. Use for any scRNA-seq workflow, including deciding which cells to filter, flag, or investigate before downstream analysis.

Metabolomics pathway analysis — metabolite identification (HMDB, KEGG, ChEBI), pathway mapping (Reactome, KEGG, MetaCyc), disease associations, enzyme/gene linkage. Use for metabolite-to-pathway-to-disease connections, BridgeDb-based ID conversion, and integrating metabolomics with gene-level pathway analyses.

Aging biology, cellular senescence, and longevity research. Covers senescence markers (p16/CDKN2A, SASP, SA-beta-gal), aging hallmarks, senolytic drug discovery (dasatinib+quercetin, fisetin, navitoclax), epigenetic clocks, telomere biology, and longevity GWAS. Use for senescence-pathway analysis, age-related disease genetics, senolytic-target discovery, and centenarian-genetics queries. Distinguishes correlative vs causal evidence (knockout, intervention).

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

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

VCF and variant analysis — parsing, annotation, classification (synonymous, missense, frameshift, stop_gained), VAF filtering, coding vs non-coding categorization, multi-condition variant comparison, variant-notation conversion (SPDI/HGVS/VCF/rsID interconversion, ALFA per-ancestry allele frequencies), European Variation Archive (EVA) lookups (per-study cohort variant data, RS-accession resolution), HGVS validation/normalization (Mutalyzer), gene-specific curated variants (LOVD), canonical cross-database allele IDs (ClinGen Allele Registry), automated ACMG/AMP classification (GeneBe), principal-transcript selection (APPRIS), Ensembl linkage disequilibrium (LD) for GWAS/fine-mapping, GRCh37/GRCh38 coordinate liftover and protein/cDNA-to-genomic mapping, and Ensembl ID utilities (stable-ID version history, cross-references, region/gene feature overlap, assembly/species metadata). Use for VCF parsing, variant fraction calculations (denominator = coding subset only, NOT all variants), per-sample mutation profiling, converting a variant between SPDI/HGVS/VCF-coordinate/dbSNP-rsID representations, cross-checking a variant against EVA's raw submitted study cohorts, validating an HGVS string's syntax, looking up curated variants for a well-studied gene, resolving a variant to its ClinGen CA ID, getting an automated ACMG verdict, or picking a gene's principal transcript.

Universal data access patterns for downloading and parsing scientific data when ToolUniverse tools don't cover the source, only return metadata, or you need bulk records. Use for VCF/h5ad/BAM/SDF/GCT parsing, multi-step API workflows (search to filter to download to parse), thousands of records at once, or sources with no dedicated tool. Write Python code via Bash for every step.

Organic chemistry reasoning guide for reaction product prediction, mechanism analysis (electrophilic/nucleophilic substitution, addition, elimination, pericyclic, radical), and spectroscopy interpretation (1H/13C NMR, IR, MS). Reasons from first principles (electron flow, kinetic vs thermodynamic) rather than pattern-matching named reactions. Use for organic synthesis problems and mechanism explanations.

Generate comprehensive disease research reports covering genetics (causal genes, GWAS, OMIM), pathways (Reactome, KEGG), drugs (existing therapies, repurposing candidates), clinical trials, epidemiology (prevalence, incidence), and phenotypes (HPO). Use for full disease overviews, comprehensive disease characterization, and orphan/rare-disease profiling.