Others skills

Browse reusable Agent Skills, each with a clear purpose and practical guidance.

tooluniverse-residue-functional-mechanism-interpretation

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.

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tooluniverse-vaccine-design

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.

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tooluniverse-variant-functional-annotation

Functional annotation of protein variants — ProtVar structural/functional context, ClinVar clinical classifications, gnomAD population frequencies, CADD deleteriousness, ClinGen gene-disease validity, plus FAVOR one-call comprehensive GRCh38 annotation. Use for variant annotation pipelines, missense effect prediction, and protein-level variant interpretation with functional context.

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tooluniverse-cancer-classification

Translate free-text tumor descriptions to OncoTree codes and resolve cancer subtypes/tissue hierarchy. Cross-references UMLS/NCI vocabularies. Use for standardizing cancer-type nomenclature in EHR free-text, building cohorts in OncoKB or GDC, mapping tumor-board notes to ontology codes, and ensuring consistent terminology across cancer-genomics pipelines.

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tooluniverse-diagnostic-test-evaluation

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.

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tooluniverse-molecular-cloning

Molecular cloning assembly design — Gibson Assembly (overlap design for seamless multi-fragment joining) and Golden Gate Assembly (Type IIS / BsaI / BbsI design with unique 4-bp fusion overhangs). Use when you need to plan how to join DNA fragments into a construct, design assembly overlaps/overhangs, or decide between cloning methods. Covers the domestication (internal-site removal), overhang-uniqueness, and overlap-Tm rules. For PCR primers to generate the fragments, see tooluniverse-primer-design.

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tooluniverse-pharmacovigilance

Drug safety and adverse event analysis — FAERS spontaneous-report mining, FDA black-box warnings, signal detection (PRR, ROR, IC), risk factors by demographic/comorbidity, and label change tracking. Use for post-market safety surveillance, AE signal investigation, drug-AE association strength scoring, and pharmacovigilance reports.

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tooluniverse-primer-design

PCR / qPCR primer and oligo design — design forward/reverse primers for a target region (SantaLucia nearest-neighbor thermodynamics), compute melting temperature (Tm) and annealing temperature (Ta), check GC content, and screen an oligo for hairpins and primer-dimers. Use when you need primers for a sequence, want to QC an existing primer pair, or need the Tm of an oligo. Covers the primer-design rules (Tm matching, GC clamp, 3'-end, length) and the tools' constraint quirks.

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additive-manufacturing

Skill for additive manufacturing process selection, design optimization, and build preparation

1.55k repo starsObserved in 2 repos
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