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SkillsMP has collected 374 skills from mims-harvard/ToolUniverse. Open a skill to review its source and details.
Showing 40 of 374 collected skills.
Install and configure ToolUniverse for any use case — MCP server (chat-based), CLI (command line with 14 subcommands), or Python SDK (Coding API with 3 calling patterns). Covers uv/uvx setup, MCP configuration for 12+ AI clients (Cursor, Claude Desktop,…
Install and configure ToolUniverse for any use case — MCP server (chat-based), CLI (command line with 14 subcommands), or Python SDK (Coding API with 3 calling patterns). Covers uv/uvx setup, MCP configuration for 12+ AI clients (Cursor, Claude Desktop,…
Install and configure ToolUniverse for any use case — MCP server (chat-based), CLI (command line with 14 subcommands), or Python SDK (Coding API with 3 calling patterns). Covers uv/uvx setup, MCP configuration for 12+ AI clients (Cursor, Claude Desktop,…
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…
Find and evaluate research datasets for any scientific question. Maps research questions to required study designs (longitudinal vs cross-sectional, observational vs experimental, single-cohort vs multi-cohort). Use when the user asks 'find data about X',…
End-to-end observational epidemiology analysis — from research question (PECO Population/Exposure/Comparator/Outcome) to publication-ready statistical report. Covers cohort/case-control/cross-sectional design, regression with confounders, propensity scoring,…
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…
Spatial transcriptomics analysis — Visium, MERFISH, seqFISH, Slide-seq. Maps gene expression to tissue architecture, identifies spatially variable genes (SVGs), tissue-domain segmentation, and cell-cell interaction inference. Use for spatial gene-expression…
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…
Answer biomedical FACTUAL / recall / multiple-choice questions by querying ToolUniverse database tools instead of answering from memory. Triggers on any 'which gene/drug/variant/disease/pathway/miRNA/TF...' lookup, any question phrased 'according to…
Find and evaluate research datasets for any scientific question. Maps research questions to required study designs (longitudinal vs cross-sectional, observational vs experimental, single-cohort vs multi-cohort). Use when the user asks 'find data about X',…
End-to-end observational epidemiology analysis — from research question (PECO Population/Exposure/Comparator/Outcome) to publication-ready statistical report. Covers cohort/case-control/cross-sectional design, regression with confounders, propensity scoring,…
Phylogenetic analysis — de novo multiple sequence alignment (Clustal Omega/MUSCLE/MAFFT via EBI_msa_align) and neighbour-joining/UPGMA tree building (EBI_build_phylogenetic_tree) from your own sequences, plus tree analysis, treeness, saturation (PhyKIT),…
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…
ToolUniverse plugin router. STEP 1 BEFORE ANY ANALYSIS: if the data folder contains `*_executed.ipynb`, run `tu run read_executed_notebook '{"data_folder":"<path>","search":"<keyword>"}'` to extract its cell outputs and apply EVERY filter/sample-exclusion the…
Spatial transcriptomics analysis — Visium, MERFISH, seqFISH, Slide-seq. Maps gene expression to tissue architecture, identifies spatially variable genes (SVGs), tissue-domain segmentation, and cell-cell interaction inference. Use for spatial gene-expression…
Therapeutic antibody engineering and optimization, lead-to-clinical-candidate. Covers sequence humanization (germline alignment, framework retention), affinity maturation, developability (aggregation, stability, PTMs), structure modeling (AlphaFold/PDB CDR…
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…
Drug regulatory and approval research — FDA substance registry, ATC/EPC classification, EMA decisions, generic-drug status, FDA Orange Book exclusivity, NDA/BLA pathways. Use for jurisdiction-aware approval status (FDA vs EMA), generic vs brand availability,…
Ecology, biodiversity, and conservation biology research — species identification (GBIF, NCBI Taxonomy), invasive species impact, ecosystem dynamics, conservation status (IUCN), niche ecology. Use for biodiversity questions, species comparison, invasion…
Genomics and epigenomics analysis: DNA methylation (CpG, 5mC, 5hmC, bisulfite, RRBS), m6A RNA modification (MeRIP-seq), ChIP-seq peaks, ATAC-seq accessibility, histone modifications, chromatin state, multi-omics integration. Combines pandas/scipy/pysam…
Molecular cloning, in both directions. DESIGN — Gibson Assembly (overlap design for seamless multi-fragment joining) and Golden Gate Assembly (Type IIS / BsaI / BbsI / Esp3I / BsmBI / SapI design with unique 4-bp fusion overhangs). ANALYSIS — work out what an…
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…
Analyze NIH grant portfolios and funding history using the OpenNIH FY1985-present corpus, then connect grants to investigators, institutions, publications, clinical trials, patents, targets, or drugs with ToolUniverse. Use for NIH grant discovery, topic or…
Plant genomics and biology research — PlantReactome pathways, Ensembl Plants gene structure, POWO species taxonomy, UniProt annotation, KEGG plant pathways. Handles polyploidy (wheat hexaploidy etc.) and homeologous gene copies. Use for crop-gene annotation,…
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…
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…
Transcription factor binding, cis-regulatory elements (cCREs), chromatin accessibility, and regulatory annotation using JASPAR (motifs), ENCODE (cCREs, ChIP-seq), RegulomeDB (regulatory variant scoring), UCSC — plus sequence-based deep-learning prediction of…
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…
Clinical variant interpretation from raw variant calls to ACMG-classified recommendations with structural impact analysis. Use for VUS classification, pathogenicity assessment with cited criteria, structure-based variant impact (AlphaFold/PDB),…
Therapeutic antibody engineering and optimization, lead-to-clinical-candidate. Covers sequence humanization (germline alignment, framework retention), affinity maturation, developability (aggregation, stability, PTMs), structure modeling (AlphaFold/PDB CDR…
Install, set up, verify, update, pin, uninstall, or troubleshoot the ToolUniverse plugin on Google Antigravity (AGY / Antigravity IDE / Antigravity 2.0). ALWAYS consult this skill for any of those — don't answer from memory, because the exact CLI name (agy),…
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…
Drug regulatory and approval research — FDA substance registry, ATC/EPC classification, EMA decisions, generic-drug status, FDA Orange Book exclusivity, NDA/BLA pathways. Use for jurisdiction-aware approval status (FDA vs EMA), generic vs brand availability,…
Ecology, biodiversity, and conservation biology research — species identification (GBIF, NCBI Taxonomy), invasive species impact, ecosystem dynamics, conservation status (IUCN), niche ecology. Use for biodiversity questions, species comparison, invasion…
Genomics and epigenomics analysis: DNA methylation (CpG, 5mC, 5hmC, bisulfite, RRBS), m6A RNA modification (MeRIP-seq), ChIP-seq peaks, ATAC-seq accessibility, histone modifications, chromatin state, multi-omics integration. Combines pandas/scipy/pysam…
Molecular cloning, in both directions. DESIGN — Gibson Assembly (overlap design for seamless multi-fragment joining) and Golden Gate Assembly (Type IIS / BsaI / BbsI / Esp3I / BsmBI / SapI design with unique 4-bp fusion overhangs). ANALYSIS — work out what an…
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…
Analyze NIH grant portfolios and funding history using the OpenNIH FY1985-present corpus, then connect grants to investigators, institutions, publications, clinical trials, patents, targets, or drugs with ToolUniverse. Use for NIH grant discovery, topic or…
Plant genomics and biology research — PlantReactome pathways, Ensembl Plants gene structure, POWO species taxonomy, UniProt annotation, KEGG plant pathways. Handles polyploidy (wheat hexaploidy etc.) and homeologous gene copies. Use for crop-gene annotation,…