All Skills

Set up, launch, validate, and troubleshoot the AF3-torch ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

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

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

Set up, launch, validate, and troubleshoot the Human expert feedback 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.

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.

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 ChromBPNet 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.

Set up, launch, validate, and troubleshoot the Profluent E1 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

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.

Transcription factor binding, cis-regulatory elements (cCREs), chromatin accessibility, and regulatory annotation using JASPAR (motifs), UniBind, ENCODE (cCREs, ChIP-seq), RegulomeDB (regulatory variant scoring), UCSC, and the Ensembl Regulatory Build (motif instances, evolutionarily constrained elements, TF binding matrices) — plus sequence-based deep-learning prediction of regulatory activity and non-coding variant effects (AlphaGenome, Enformer, Borzoi, ChromBPNet, Evo 2). Use for regulatory element annotation, TF-binding-site prediction, regulatory-region functional impact assessment, and predicting how a non-coding variant or a raw DNA sequence affects expression/chromatin/accessibility. Use this whenever a user asks what regulates a gene, whether a SNP hits a regulatory element, or to predict a non-coding variant's functional effect from sequence.

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

Continuous improvement system for ToolUniverse tools, skills, and plugin. Run benchmarks, diagnose failures, route fixes to devtu skills, retest. Use after skill optimization, tool additions, or as regression check.

Given a set of residues in a protein, explain WHY they are functionally critical by combining structural context (binding interface, ligand pocket, core, secondary structure), UniProt features (active sites, binding sites, PTM sites, disulfides), optional SAE feature evidence, and optional DMS data. Accepts residues from any source: DMS hotspots (top-K by max effect), ClinVar recurrent variants, literature-reported hot regions, evolutionarily conserved positions, or user-curated lists. Returns a per-cluster mechanism call: catalytic / ligand-binding / interface / structural-core / PTM / regulatory / unknown.

Set up, launch, validate, and troubleshoot the RFD4-Proteina ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

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

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 AlphaFold 2 initial-guess (dl_binder_design) ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

Metabolomics research — metabolite identification, study analysis, and database searches across HMDB, MetaboLights, Metabolomics Workbench, KEGG. Use for annotating mass-spec features to known metabolites, finding metabolomics studies of a disease, and structured metabolomics research reports with metabolite-pathway mapping.

Set up, launch, validate, and troubleshoot the AlphaProtein Novo (de novo enzyme design) ToolUniverse remote tool. Use when deploying or auditing this implementation.

AI-driven patient-to-trial matching for precision oncology and rare-disease care. Transforms a patient's molecular profile (mutations, biomarkers, expression) and clinical state into ranked clinical-trial recommendations with evidence tiers. Searches ClinicalTrials.gov, the EU CTIS register (European/EEA trials), AND the ISRCTN registry (UK/international) plus cross-references CIViC, OpenTargets, ChEMBL, and FDA labels. Use for matching patients to trials by genotype, biomarker-driven trial selection, trial-eligibility scoring, and finding trials across the US, Europe, and the UK.

Generate a full clinical trial protocol document (ICH E6(R2)/FDA-style) for a drug or medical device, including background, objectives/endpoints, study design, population/eligibility, intervention details, assessment schedule, statistical analysis plan with sample-size justification, safety monitoring, and regulatory/ethical sections. Use when users say "generate a clinical trial protocol", "draft a protocol for [drug/device]", "write up the study design as a protocol document", "create an FDA submission protocol", "help me write section X of a trial protocol", or "calculate the sample size for this trial". Produces a stakeholder-ready Markdown deliverable, not a feasibility score.

Microbiome and metagenomics analysis using MGnify, GTDB taxonomy, ENA sequencing data, and EuropePMC literature. Covers taxonomic classification, genome quality assessment, biome-clinical phenotype linkage, and pathway interpretation. Use for amplicon/shotgun metagenomics study analysis.