All Skills

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

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

Set up, launch, validate, and troubleshoot the OpenFold3 OpenBind-0 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

Comprehensive ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) profiling for drug candidates. Integrates ADMET-AI predictions, SwissADME drug-likeness, PubChemTox experimental toxicity, ChEMBL clinical data, Lipinski rule-of-five, and CYP interaction data. Use for drug-likeness assessment, BBB penetration, bioavailability, hepatotoxicity prediction, ADME/PK profiling, or screening compound libraries before lab testing.

KEGG-based disease-drug-variant network research. Connects diseases to causal genes, drugs to molecular targets, and variants to pathways using KEGG's editorially curated databases (KEGG Disease, Drug, Network, Variant, Pathway). Use for drug repurposing via shared pathways, mechanistic disease-gene-drug networks, and pathway-based target discovery. Distinguishes direct (binding) vs indirect (pathway co-membership) drug-target relationships.

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 Milo ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

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.

Interpret a missense variant via ESMC-6B Sparse Autoencoder (SAE) feature activations. For a given protein + variant, computes which interpretable SAE features (catalytic, ligand-binding, PTM, structural motif, domain, etc.) are lost or gained at the mutation site. Use when standard pathogenicity scores (AlphaMissense, ClinVar) say a variant is damaging but you need a MECHANISTIC explanation — e.g. 'why is this variant LoF?' Complements (does not replace) variant-interpretation and variant-to-mechanism skills, which focus on ACMG classification or regulatory mechanism.

Check PersonalizationMCP integration health and MCP tool exposure profile. Use when users ask whether setup/config is correct, whether credentials are ready, or to quickly diagnose platform readiness before deeper tasks.

Webcrawl 404 Audit Instructions

Review scientific manuscripts, abstracts, methods, statistical analyses, results, discussions, protocols, and experimental designs using calibrated rubrics and prioritized revision advice. Use for journal-style peer review, study-design scoring, methodology or statistics critique, novelty and literature-context assessment, interpretation checks, scientific writing review, reproducibility review, ethics screening, protocol optimization, or a combined manuscript review. This is the host-agent replacement for the corresponding ToolUniverse AgenticTool reviewers and does not require a ToolUniverse backend LLM API.

HLA gene-family analysis and MHC-peptide binding for transplant compatibility, vaccine epitope coverage, and cancer immunotherapy. Uses IMGT (HLA polymorphism), IEDB (epitope-MHC binding), UniProt (annotation), DGIdb (druggability). Use for HLA typing/imputation review, vaccine HLA coverage, and immunotherapy prediction biomarkers (HLA-LOH, neoantigen presentation).

Help the user publish one tool from their shared computer to ToolUniverse so other scientists' AI scientists can find and run it, choosing whether only they, specific colleagues, or everyone can use it. Prepares and tests the tool for them; the user makes the final Publish click. Use when the user says "publish my tool", "put my model in Discover", "let anyone use this tool", "let only my collaborators use this tool", or "unpublish my tool".

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.

Set up, launch, validate, and troubleshoot the GPN-Star ToolUniverse remote tool (single-nucleotide variant effect scores from a multi-species-alignment language model) 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.

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.

Spatial transcriptomics analysis — Visium, MERFISH, seqFISH, Slide-seq. Maps gene expression to tissue architecture, identifies spatially variable genes (SVGs), tissue-domain segmentation, and cell-cell interaction inference. Use for spatial gene-expression questions, tissue architecture analysis, and SVG identification.

Protein-protein interaction (PPI) network analysis — STRING (predicted + experimental), BioGRID (curated), SASBDB (small-angle scattering), Complex Portal (curated complex membership and stoichiometry, includes CORUM data). Distinguishes physical interactions (binding) from functional associations (co-expression, co-regulation). Use for interactome queries, complex partner identification, curated complex composition lookup, and pathway-level interaction analysis.

Biological sequence analysis — gene/protein sequence retrieval (NCBI, Ensembl, UniProt), nucleotide/protein search, ortholog discovery, and FASTQ QC + alignment workflows (Trimmomatic, BWA, samtools, coverage depth). Use for sequence retrieval, sequence comparison, FASTQ QC analysis, and read alignment pre-processing.

Run and review iterative protein binder design campaigns with multiple model families, structural and glycan checks, conditional pH hypotheses, resource-aware computation, and competition submission preparation. Use for ongoing candidate optimization or interpreting conflicting design evidence; not for simple structure retrieval or measured assay analysis.

Map environmental and industrial chemicals to adverse outcome pathways (AOPs) — molecular initiating event to organ-level toxicity. Uses AOPWiki, GHS classification, IARC carcinogen status, and LD50 data. Use for environmental/industrial chemical risk assessment, regulatory-grade hazard characterization, and AOP stressor mapping. Distinct from drug-safety analysis (use tooluniverse-pharmacovigilance for drugs).

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. Produces 5-tier verdict (Pathogenic / Likely Pathogenic / VUS / Likely Benign / Benign) with cited evidence per criterion. Use for variant interpretation, VUS resolution, and pathogenicity assessment. Combines ClinVar, gnomAD, computational predictors, and gene-mechanism context.