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SkillsMP a collecté 339 skills depuis mims-harvard/ToolUniverse. Ouvrez un skill pour examiner sa source et ses détails.
mims-harvard/ToolUniverseAffichage de 40 skills collectés sur 339.
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
Post-translational modification (PTM) analysis — phosphorylation, ubiquitination, acetylation, glycosylation, methylation. Uses iPTMnet (sites + enzymes), ProtVar (functional consequences), UniProt (baseline), STRING, ELM (linear motifs),…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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,…
Langue du texte source : anglais
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,…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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,…
Langue du texte source : anglais
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 /…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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,…
Langue du texte source : anglais
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,…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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,…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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),…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais