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Build local BLAST databases and run searches using NCBI BLAST+ command-line tools. Use when running >50 queries, building custom databases with -parse_seqids and -taxid, downloading prebuilt NCBI databases via update_blastdb.pl, choosing -task variants (megablast/dc-megablast/blastn/blastn-short), tuning soft/hard masking, scaling threads, or extracting hits with blastdbcmd. Encodes BLAST v5 vs v4 database format, taxonomy filtering, makeblastdb pitfalls.

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Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables. Use when batch-converting Ensembl IDs to other namespaces (HGNC, RefSeq, UniProt, Entrez), pulling gene coordinate tables for thousands of genes, building ortholog wide-tables across species, or replacing slow Ensembl REST loops with one-shot bulk export. Encodes BioMart's XML query format, R biomaRt vs Python pybiomart trade-off, mart-vs-dataset hierarchy, and the URL endpoint that's BioMart-specific (separate from rest.ensembl.org).

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Visualize biological networks (PPI, gene-regulatory, co-expression, pathway) with layout algorithm choice (ForceAtlas2, Fruchterman-Reingold, Kamada-Kawai, hive plots), edge bundling, community-based coloring, and reproducible seeds using NetworkX, PyVis, igraph, and Cytoscape automation. Use when rendering biological networks for static publication, interactive HTML exploration, or Cytoscape-format export.

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Build publication-quality figures with matplotlib using the object-oriented Figure/Axes API, constrained_layout, rcParams customization, TrueType (Type-42) font embedding for journal submission, and CVD-safe palettes. Covers seaborn integration, common chart types, axis formatting, and the small gotchas that distinguish reproducible matplotlib from notebook scratch. Use when producing publication figures in Python — RNA-seq scatter, single-cell embeddings, generic biological plotting.

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Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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Constructs and validates polygenic risk scores using LDpred2-auto, SBayesRC, MegaPRS, PRS-CS, PROSPER, MUSSEL, BridgePRS, JointPRS, PRSmix, or PGS Catalog Calculator with ancestry-aware reference panels (HapMap3, UKB-LD), Pejaver-style calibration, and PRS-RS reporting standards. Use when computing PRS for cohorts, applying Whiffin-style absolute-risk transformation, assessing cross-ancestry portability (Martin 2017 / Ding 2023 continuous ancestry), or auditing PRS manuscripts against the 22-item PRS-RS reviewer checklist.

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Reads, validates, and prepares CDISC SDTM and ADaM clinical trial data for analysis. Covers SDTM domain joins (DM, AE, EX, VS, LB, DS), ADaM architecture (ADSL, BDS, OCCDS, ADTTE) with traceability, treatment-emergent AE conventions, baseline derivation, SUPPQUAL/NSV handling, Define-XML 2.1, and Pinnacle 21 / CORE validation. Use when working with clinical trial datasets in CDISC SDTM/ADaM format, preparing analysis-ready data, or validating for regulatory submission.

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Designs Bayesian clinical trials including Phase I dose-finding (BOIN, CRM, EWOC, mTPI-2), meta-analytic-predictive (MAP) priors with robust mixtures for external data borrowing, EXNEX for basket trials, hierarchical models for safety AE (Berry-Berry), Bayesian platform trials (I-SPY 2, GBM AGILE, REMAP-CAP), and posterior probability stopping rules. Covers FDA Bayesian Devices Guidance (2010), FDA Bayesian Methodology in Drugs Draft (January 2026), BOIN Fit-for-Purpose qualification (December 2021), and Project Optimus dose-optimisation. Use when designing dose-finding studies, platform trials, or sensitivity analyses with informative priors.

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Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis via mmpdb, R-group decomposition, Free-Wilson analysis, scaffold hopping, and chemotype-aware ML train/test splits. Use when identifying chemotype clusters in a library, deriving SAR transformation rules, decomposing series into R-groups, performing scaffold-balanced QSAR splits, or planning analog campaigns.

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Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware torsion preferences. Provides explicit decision rules for single vs ensemble conformer use, RMSD pruning, energy windows, conformer count, and force-field choice. Use when preparing 3D ligands for docking, generating descriptor input for 3D QSAR, or sampling macrocycle/peptide conformational ensembles.

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Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, MMTF) using RDKit and Open Babel with rigorous handling of aromaticity perception, stereochemistry, implicit/explicit hydrogens, kekulization, and salt/fragment separation. Use when loading chemical libraries, debugging parse failures, or preparing molecules for downstream standardization, descriptor calculation, or docking.

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View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure.

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Use when users need bioinformatics analysis on the NCPGR cluster, especially when converting analysis requests into local software choices, resource plans, and LSF job scripts.

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Creates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose, condition-grouped overlays), rmats2sashimiplot (rMATS-output-aware), MAJIQ-VOILA (LSV posteriors interactive HTML), leafviz (leafcutter clusters Shiny), Jutils (tool-agnostic heatmaps and sashimi for rMATS/leafcutter/SUPPA2/MAJIQ output), or pyGenomeTracks (multi-track publication figures). Tool choice depends on the upstream differential-splicing tool's output format and the publication vs interactive use case. Use when visualizing specific splicing events, validating differential splicing calls, or producing publication-quality figures.

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Use this skill to understand when electronic records are acceptable to FMCSA inspectors. Covers PDF, original-format, and search-ability requirements.

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Use this skill when the user asks about Motor Vehicle Records (MVRs), 49 CFR 391.25 annual MVR review, continuous MVR monitoring services (SambaSafety, Foley, etc.), state MVR fees, what to look for on an MVR, CDLIS (Commercial Driver License Information System), or how often MVRs must be pulled. Cite 49 CFR 391.25 and 391.27.

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Use this skill when the user asks where to find specific information at fmcsa.dot.gov — the SAFER (Safety and Fitness Electronic Records System), Carrier Snapshot, Compliance Safety Accountability (CSA) data, PSP (Pre-Employment Screening Program), Clearinghouse, Unified Carrier Registration (UCR), MCS-150 update, complaints, DataQs, and the FMCSA Portal login. Reference fmcsa.dot.gov.

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Use this skill when the user asks about Environmental Health & Safety (EHS) for trucking — fuel spill response, hazmat release reporting, EPA + state environmental reporting, emergency contact information (CHEMTREC), environmental impairment liability insurance, and how to handle a CMV-related environmental incident. Cite 40 CFR + 49 CFR 174.6.

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Use this skill when the user asks about cybersecurity for a trucking carrier — protecting ELD data, customer information, financial systems, EDI integrations, fleet telematics, ransomware risk, vendor / shipper data sharing, incident response, and FMCSA cyber-recommendations. Reference NIST + CISA cybersecurity frameworks.

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Use this skill when the user asks about FCRA adverse action procedures — what to do when a background check (MVR, criminal, drug test) returns information that may lead to denying employment or terminating a CDL driver. Covers the 5-business-day pre-adverse-action notice, FCRA Summary of Rights, final adverse action notice, state-specific add-ons (CA, NY, etc.), and how to handle disputes. Cite 15 USC § 1681 (FCRA) and 49 CFR 391.

日本語の概要は準備中です。原文の説明を表示しています。

Use this skill to maintain a compliant DOT accident register. Covers § 390.15 requirements, what's recorded, retention period.

日本語の概要は準備中です。原文の説明を表示しています。

Comprehensive overview of ALL Coval platform resources, their hierarchy, relationships, API endpoints, and ID formats. Use when user asks about Coval resources, data model, how things relate, what endpoints exist, or needs context about the platform structure before making API calls.

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Run the full static analysis suite — ruff lint, ruff format check, pyright type check, auth analysis, license headers. Use before committing or to verify code quality after changes.

日本語の概要は準備中です。原文の説明を表示しています。

Image optimization analysis for SEO and performance. Checks alt text, file sizes, formats, responsive images, lazy loading, CLS prevention, image SERP rankings (via DataForSEO), and image file optimization (WebP/AVIF conversion, IPTC/XMP metadata injection). Use when user says "image optimization", "alt text", "image SEO", "image size", "image audit", "optimize images", "image metadata", "image SERP", "convert to webp", or "image file optimize".

日本語の概要は準備中です。原文の説明を表示しています。