All Skills

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

Deep literature review — PubMed, EuropePMC, bioRxiv preprints, citation networks, evidence synthesis. Disambiguates queries, runs collision-aware searches, grades evidence T1-T4, and produces structured reports. Use for systematic literature review, meta-analysis evidence collection, and detailed answer-with-citations workflows.

Meta-analytic decoding of human fMRI coordinates using the Neurosynth coordinate database (14,371 studies, ~3,228 cognitive/neuroscience terms) — given an MNI brain coordinate, statistically identify which cognitive terms are over-represented in studies reporting activation there ("reverse inference"); given a term, find the studies and coordinates most associated with it ("forward" lookup). Use when someone asks "what does this brain coordinate/region do", "decode this fMRI activation peak", "what terms are associated with [MNI coordinate]", "find studies about [cognitive term] and their activation coordinates", or "reverse-infer cognitive function from a brain location". This is real local analysis on a downloaded, cached coordinate database — not a live API — following ToolUniverse's honesty-contract pattern (real computed statistics, no fabricated term associations).

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 analysis), immunogenicity prediction, and manufacturing feasibility. Use for biologic-drug optimization, mAb design review, biosimilar engineering, and clinical-precedent comparison.

Set up, launch, validate, and troubleshoot the MACS3 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

Microscopy and quantitative imaging analysis — colony morphometry, fluorescence intensity quantification, cell-count statistics, dose-response curves, and ANOVA/Dunnett on image-derived measurements. Uses pandas/numpy/scipy/scikit-image. Use for analyzing tabular outputs from CellProfiler/ImageJ, image-derived measurement statistics, and image-based assay quantification.

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

Add custom local tools to ToolUniverse alongside the 1000+ built-in tools. Covers JSON-config tools (simplest, no code), Python class tools (REST/SOAP/GraphQL APIs, computational logic), and best-practices for return schemas. Use for wrapping new APIs, adding domain-specific computations, or contributing tools to the registry.

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.

Orchestrate the full ToolUniverse self-improvement cycle: discover APIs, create tools, test with researcher personas, fix issues, optimize skills, and push via git. References and dispatches to all other devtu skills. Use when asked to: run the self-improvement loop, do a debug/test round, expand tool coverage, improve tool quality, or evolve ToolUniverse.

Detect and auto-install missing ToolUniverse research skills. Checks common Claude Code/Cursor/Codex skill directories for the canary file, and installs any missing skills if none found. Use when the plugin's research skills aren't loading, when migrating between clients, or when verifying a skill installation.

Configure and use Bilibili in PersonalizationMCP. Trigger when users need cookie-based credential setup, validation, video search, or BVID detail lookup.

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 identification, virtual screening, target-to-compounds workflows, and lead-finding before commit-to-medchem.

Protein structure retrieval from RCSB PDB, PDBe, AlphaFold, SWISS-MODEL, 3D-Beacons (cross-provider structure aggregator), and PDB-REDO (re-refined X-ray structures), with disambiguation, quality assessment (resolution, R-factor, pLDDT, coverage), and metadata. Distinguishes high-quality experimental (X-ray under 2 Angstrom) vs predicted vs homology-model vs medium-quality structures. Use for fetching protein structures, structure-quality comparison, batch model-availability checks across a gene list, checking every structure provider at once, and selecting structures for drug design or modeling.

Configure and use Spotify in PersonalizationMCP. Trigger when users need Spotify API credential setup, token validation, or recent listening summaries.

Set up, launch, validate, and troubleshoot the BioEmu-2 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

Evaluate the human safety liability of knocking down, knocking out, degrading, or pharmacologically inhibiting a gene. Use for gene safety scoring, on-target toxicity assessment, essentiality and genetic-constraint review, critical-organ expression analysis, or deciding whether a target needs partial, transient, or tissue-specific modulation.

Unified onboarding entry for PersonalizationMCP credentials. Use when users want to set up one or more platforms from scratch, migrate credentials, or fix partial configuration across Steam, YouTube, Bilibili, Spotify, and Reddit.

Structural biology plus proteomics integration for drug target validation. Combines PDB experimental structures, AlphaFold predictions, GPCRdb, SAbDab antibody structures, ProteinsPlus binding-site prediction, BindingDB ligand-affinity data, BMRB NMR data, CATH/InterPro fold classification, intrinsic-disorder prediction (MobiDB/DisProt/IUPred3), membrane-protein topology (OPM/TopDB/PDBTM/ChannelsDB), enzyme catalytic-site data (M-CSA), PDBe ligand/compound chemistry, and MD simulation trajectory metadata (MDDB). Use for druggability assessment, binding-site characterization, ligand-pocket analysis, structural-confidence scoring (resolution, pLDDT), antibody-target interface analysis, disordered-region assessment, membrane-protein topology, catalytic-mechanism lookup, and finding published MD simulations for a target.

How to use ToolUniverse Connect (connect.aiscientist.tools), the hosted ToolUniverse service, and when to use it instead of ToolUniverse installed on this computer. Use when the user asks how to use ToolUniverse or ToolUniverse Connect, how to connect Claude, Claude Code or Codex, whether to use the hosted service or a local install, why a tool says a login or API key is missing and where to add it, how to share a model or script with colleagues, how to use a colleague's computer or a TU-SHARE code, how to publish a tool, or when ToolUniverse tools are missing, signed out or not connecting.

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.

Discover and characterize cancer radiology imaging cohorts from The Cancer Imaging Archive (TCIA) — list public collections (e.g. LIDC-IDRI, TCGA-GBM, TCGA-LUAD, TCGA-BRCA), enumerate patients/subjects and studies within a collection, browse DICOM series by modality (CT, MR, PT, CR, DX, US, NM) or body part (CHEST, BRAIN, ABDOMEN, ...), pull series-level DICOM metadata and scanner manufacturer, estimate download size before pulling data, and enumerate individual DICOM instance (slice) UIDs within a series. Use when someone asks to "find a CT/MRI/PET imaging cohort for [cancer type]", "how many patients/studies/series are in [TCIA collection]", "what imaging modalities/body parts/scanners does [collection] have", "look up DICOM series metadata for [SeriesInstanceUID]", "estimate the size of this TCIA series before downloading", or "build a radiology imaging research cohort". NOT for microscopy/cell imaging quantification (use tooluniverse-image-analysis), NOT for actual DICOM pixel data analysis, segmentation, or diagnosis (TCIA tools here return metadata only — no pixel access), NOT for tumor genomic/omics data (use tooluniverse-cancer-genomics-tcga).

Strategic clinical trial design feasibility assessment. Analyzes 6 dimensions (endpoint, population, comparator, effect size, duration, regulatory pathway) using precedent trials and FDA guidance. Produces enrollment projections, endpoint recommendations, and approval-pathway analysis. Use for trial-protocol design, power/sample-size estimation, comparator selection, and FDA submission strategy. Driven by precedent-based reasoning rather than first-principles math.

Cross-species genetic analysis using model organism databases (MGI mouse, IMPC systematic knockout phenotyping, ZFIN zebrafish, FlyBase fruit fly, WormBase worm, SGD budding yeast plus protein-domain/PTM/literature detail, PomBase fission yeast, RGD rat, GeneNetwork systems-genetics/eQTL panels, HumanMine/MouseMine cross-species data-warehouse search, GBIF taxonomy) plus VEuPathDB for eukaryotic pathogens (Plasmodium, Toxoplasma, fungi, vectors). Maps human genes to orthologs, retrieves phenotype/expression/functional data, assesses gene function conservation, and identifies the best animal model for studying a human gene or disease.