All Skills

Pattern System - Core Agent Principles

Spec Design Command

Set up, launch, validate, and troubleshoot the Monocle 3 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

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

Discover novel small-molecule binders for protein targets using structure-based and ligand-based screening. Covers druggability assessment, known-ligand mining (ChEMBL, BindingDB), similarity expansion, ADMET filtering, and synthesis feasibility. Use for hit identification, virtual screening, target-to-compounds workflows, and lead-finding before commit-to-medchem.

Set up, launch, validate, and troubleshoot the mosaic (Boltz-2 binder hallucination) ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

Cross-species gene comparison and ortholog analysis. Integrates Ensembl Compara orthologs, NCBI Gene, UniProt, OLS, Monarch, and OpenTargets to identify orthologs, paralogs, sequence conservation, functional conservation across species, and lineage-specific gene gains/losses. Use for phylogenetic gene tracing, model-organism mapping, and evolutionary-genomics queries.

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.

Post-translational modification (PTM) analysis — phosphorylation, ubiquitination, acetylation, glycosylation, methylation. Uses iPTMnet (sites + enzymes), ProtVar (functional consequences), UniProt (baseline), STRING, ELM (linear motifs), MassIVE/ProteomeXchange (experimental), and the EBI Proteins API (mutagenesis, MS-proteomics/HPP peptide evidence, antigenic regions, genomic coordinates, protein-level variant lookup by accession/dbSNP/HGVS) as a cross-validation source. Use for PTM site annotation, kinase-substrate identification, and PTM-disease associations.

Set up, launch, validate, and troubleshoot the ColabFold (AlphaFold2-Multimer) ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

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.

Website Gopher Service

Set up, launch, validate, and troubleshoot the ProGen2 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

Set up, launch, validate, and troubleshoot the cell2location ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

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

Website File Type Audit Instructions

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.

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.

Share tools that live on this computer (the user's own Python function, script or notebook code, a model, a program they already run, or ToolUniverse's reviewed GPU models) so the user's and their colleagues' AI scientists can use them through ToolUniverse. You do the work; the user only answers questions and clicks Allow once in a browser. Use when the user says things like "share my model with my lab", "let my colleague use this script", "make this function a tool", "put my GPU models on ToolUniverse", or "keep my tool running".

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.

Find and retrieve proteomics datasets from MassIVE, ProteomeXchange, PRIDE Archive, and the NCI Proteomics Data Commons (PDC). Search by species, keyword, accession, or protein; retrieve detailed metadata (instruments, publications, species, PTMs studied), real file-download URLs (PRIDE), or quantitative abundance matrices with clinical linkage (PDC/CPTAC). Use for locating public proteomics datasets to reanalyze, comparing instrument/protocol coverage across studies, pre-download dataset evaluation, and finding every dataset that identified a specific protein.

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.

Set up, launch, validate, and troubleshoot the scANVI 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.