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SkillsMP ha recopilado 339 skills de mims-harvard/ToolUniverse. Abre una skill para revisar su origen y sus detalles.
mims-harvard/ToolUniverseMostrando 40 de 339 skills recopiladas.
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…
Idioma del texto original: inglés
Post-market safety surveillance and recall/adverse-event RETRIEVAL across the full spectrum of FDA-regulated products that are NOT covered by the drug-AE signal skills: medical devices, food / dietary supplements / cosmetics, veterinary drugs, and drug supply…
Idioma del texto original: inglés
Propose the mechanism by which a missense variant causes loss-of-function (LoF), synthesizing evidence from 5 independent layers: AlphaMissense pathogenicity, AlphaFold structural context, ESMC sequence likelihood, SAE feature disruption, and DynaMut2…
Idioma del texto original: inglés
Post-translational modification (PTM) analysis — phosphorylation, ubiquitination, acetylation, glycosylation, methylation. Uses iPTMnet (sites + enzymes), ProtVar (functional consequences), UniProt (baseline), STRING, ELM (linear motifs),…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
Given a PDB structure, produce a per-residue annotation table: which residues sit at a binding interface (vs a partner chain), which line a ligand pocket, which are buried (core) vs solvent-exposed (surface), and optionally secondary structure. This is the…
Idioma del texto original: inglés
Protein 3D structure prediction from sequence — ESMFold de novo prediction, AlphaFold database retrieval, experimental structures from RCSB, ProtVar variant impact assessment, ProtParam sequence properties. Use for structure prediction when no experimental…
Idioma del texto original: inglés
Protein structure retrieval from RCSB PDB, PDBe, and AlphaFold with disambiguation, quality assessment (resolution, R-factor, pLDDT), and metadata. Distinguishes high-quality experimental (X-ray under 2 Angstrom) vs predicted vs medium-quality structures. Use…
Idioma del texto original: inglés
AI-guided de novo protein design — RFdiffusion backbone generation, ProteinMPNN sequence design, structure validation (pLDDT, pTM, MPNN scores). Use for designing therapeutic protein binders, novel scaffolds, enzyme variants, and miniprotein/protein-interface…
Idioma del texto original: inglés
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,…
Idioma del texto original: inglés
Find and retrieve proteomics datasets from MassIVE and ProteomeXchange. Search by species, keyword, or accession; retrieve detailed metadata (instruments, publications, species, PTMs studied). Use for locating public proteomics datasets to reanalyze,…
Idioma del texto original: inglés
Rare disease genomics — disease identification (Orphanet), causative gene discovery, gene-disease validity (GenCC), variant interpretation (ClinVar), and translational research (ClinicalTrials.gov, drug repurposing for orphans). Use for rare-disease-gene…
Idioma del texto original: inglés
Non-coding/regulatory variant interpretation — GWAS association lookup, eQTL evidence (GTEx), chromatin state (ENCODE), regulatory variant scoring (RegulomeDB, CADD), and TF-binding disruption. Use for non-coding GWAS hit interpretation, eQTL-based gene…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
Build AI scientist systems with the ToolUniverse Python SDK for scientific research. Covers the 3 calling patterns (`tu.run` portable dict API, `tu.tools.X` function API, direct class instantiation), tool loading, batch execution, MCP server integration, and…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
Retrieve DNA/RNA/protein sequences from NCBI and ENA with disambiguation. Quality hierarchy: RefSeq (NM_/NP_) > RefSeq predicted (XM_/XP_) > GenBank submissions. Use for fetching specific sequences by accession, gene-symbol-to-sequence lookup,…
Idioma del texto original: inglés
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 /…
Idioma del texto original: inglés
Small molecule identification, characterization, and procurement — PubChem, ChEMBL, BindingDB, ADMET-AI, SwissADME, eMolecules, Enamine. Covers compound name to structure to activity to ADMET properties to commercial sourcing. Use for chemical biology, lead…
Idioma del texto original: inglés
Spatial multi-omics interpretation pipeline. Transforms spatially variable genes (SVGs), domain annotations, and tissue context into biological insights via domain-by-domain characterization, cell-type composition, spatial gene expression patterns,…
Idioma del texto original: inglés
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,…
Idioma del texto original: inglés
Structural biology plus proteomics integration for drug target validation. Combines PDB experimental structures, AlphaFold predictions, GPCRdb, SAbDab antibody structures, ProteinsPlus binding-site prediction, and BindingDB ligand-affinity data. Use for…
Idioma del texto original: inglés
Structural variant (SV) clinical interpretation: deletions, duplications, inversions, translocations, complex rearrangements. Applies ACMG-adapted criteria with ClinGen HI/TS dosage scores, gnomAD frequencies, and ClinVar evidence. Produces 5-tier…
Idioma del texto original: inglés
Systems biology and pathway analysis integrating Reactome, KEGG, WikiPathways, BioCarta, NCI-Nature Pathway Interaction Database. Multi-database pathway enrichment, protein-pathway relationships, network reasoning. Use for pathway analysis on a gene list,…
Idioma del texto original: inglés
Drug and chemical toxicity assessment via adverse outcome pathways (AOPs), real-world FAERS adverse event signals, FDA labels, and toxicogenomic associations. Triangulates molecular initiating event to cellular outcome to organ-level toxicity to clinical…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
Install, set up, verify, update, pin, uninstall, or troubleshoot the ToolUniverse plugin on OpenAI Codex. ALWAYS consult this skill for any of those — don't answer from memory, because the exact marketplace name (mims-harvard/ToolUniverse), the "codex plugin…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
Retrieve chemical compound data from PubChem and ChEMBL with disambiguation, cross-referencing, and stereochemistry handling. Use for resolving compound names to SMILES/InChI/CID/ChEMBL IDs (including OPSIN deterministic IUPAC-name-to-structure parsing),…
Idioma del texto original: inglés
Chemical safety and toxicology assessment integrating ADMET-AI predictions, CTD toxicogenomics, PubChemTox experimental data, GHS/IARC hazard classification, and exposure-context analysis. Use for chemical hazard identification, occupational/consumer-product…
Idioma del texto original: inglés
Compute and interpret validated bedside clinical risk scores and pretest probabilities for an INDIVIDUAL patient — pick the right score for the scenario, gather inputs, run the deterministic calculator tool, and read the result against an interpretation…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
Rapid pathogen characterization and drug repurposing for outbreaks. Combines pathogen genomics (NCBI, BVBRC), host immune response (IEDB), drug-target databases (ChEMBL, DGIdb), and literature surveillance (PubMed/EuropePMC). Use for emerging-pathogen…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
Genome-ASSEMBLY discovery, QC, and replicon mapping for any organism (bacteria, archaea, fungi, and beyond) using NCBI Datasets. Resolves an organism name or taxid to assemblies, picks the reference/representative or best-quality assembly, pulls assembly QC…
Idioma del texto original: inglés
Dereplicate a putative natural product and assign its chemical taxonomy. Use to answer "is [compound] a known natural product", "what microbe/organism produces [compound]", "what chemical class is [compound]", "dereplicate this metabolite (by formula/exact…
Idioma del texto original: inglés
Neuroscience research workflows: neuroanatomy, neural circuits, neurotransmitter biology, neurological/psychiatric disease genetics, neural-protein function. Uses Allen Brain Atlas, WormBase (C. elegans connectome), UniProt for neural proteins, PubMed for…
Idioma del texto original: inglés