Scientific manuscript writing knowledge: IMRAD structure, citation styles (APA/AMA/Vancouver/IEEE), figures and tables best practices, reporting guidelines (CONSORT/STROBE/PRISMA/ARRIVE), writing principles (clarity/conciseness/accuracy), field-specific terminology, venue-specific style adaptation. For LaTeX report formatting see companion assets.

Molecular docking with AutoDock Vina via Python API. Receptor/ligand preparation (Meeko + RDKit), grid box setup, docking execution, pose extraction, binding energy analysis, and batch virtual screening. Use for protein-ligand docking and hit identification.

Cross-reference chemical compound identifiers across 50+ databases (ChEMBL, DrugBank, PubChem, ChEBI, PDB, KEGG) using the UniChem REST API. Resolve InChIKeys to database-specific IDs, find all sources for a compound, discover related compounds by structural connectivity, and batch-translate compound lists between naming systems. No authentication required.

Query BRENDA Enzyme Database for kinetic parameters (Km, Vmax, kcat, Ki), enzyme classifications, substrate specificity, inhibitors, cofactors, and organism-specific enzyme data via SOAP/REST API. 80,000+ enzyme entries, 7M+ kinetic values. Requires free academic registration. For metabolic pathway modeling use cobrapy-metabolic-modeling; for metabolite structures use hmdb-database.

Build, read, validate, and modify SBML biological network models using libSBML Python API. Supports all SBML Levels (1–3), reactions with kinetic laws, species/compartments, rules (assignment/rate/algebraic), the FBC extension for flux balance analysis models, and model conversion utilities. Integrates with COBRApy, Tellurium/RoadRunner, and COPASI for simulation. Use when programmatically constructing ODE-based or constraint-based metabolic/signaling models in the standard SBML format.

Multi-Omics Factor Analysis v2 (MOFA+) with mofapy2. Jointly decompose multiple omics layers (scRNA-seq, ATAC-seq, proteomics, methylation) into latent factors that capture major sources of biological variation. Supports multi-group designs (patients, conditions). Pipeline: prepare AnnData views → create MOFA object → train → inspect variance explained → correlate factors with metadata → visualize and cluster → enrichment of top loadings.

Multi-modal single-cell analysis with muon and MuData. Joint RNA+ATAC (10x Multiome), CITE-seq (RNA+protein), and other multi-omics combinations. MuData container holds modality-specific AnnData objects with shared obs. Weighted Nearest Neighbor (WNN) graph for joint embedding, per-modality preprocessing, cross-modal factor analysis with MOFA. Use scanpy-scrna-seq for single-modality RNA analysis; use muon when combining two or more omics modalities from the same cells.

Comprehensive decision guide for analyzing omics data (transcriptomics, proteomics) using a three-tiered approach: validated pipelines first, standard workflows second, custom analysis last. Covers quality control strategies, normalization method selection, missing value imputation, statistical test selection based on data properties, and result visualization. Consult this guide when planning a bulk RNA-seq or proteomics differential analysis to choose the right tools, tests, and preprocessing steps.

Query Reactome pathway database via REST API. Pathway queries, entity retrieval, keyword search, gene list enrichment analysis, pathway hierarchy, cross-references. Content Service (pathway data) and Analysis Service (enrichment). For Python wrapper use reactome2py. For KEGG pathways use kegg-database; for protein interactions use string-database-ppi.

Query STRING REST API for protein-protein interactions (59M proteins, 20B interactions, 5000+ species). Retrieve interaction networks, perform GO/KEGG enrichment analysis, discover interaction partners, test PPI enrichment significance, generate network visualizations, and analyze protein homology for systems biology and pathway analysis.

Amazon brand protection toolkit. Detect hijackers, counterfeits, and unauthorized sellers. Includes MAP violation monitoring, trademark abuse detection, complaint templates for Brand Registry, and test buy evidence collection guides. No API key required.

Cross-platform PPC strategy planner for ecommerce businesses. Analyzes your product and margins, recommends the right advertising platforms (Google Ads, Meta Ads, TikTok Ads), calculates ROAS targets, allocates budget across channels, and generates platform-specific campaign briefs with ad copy and creative direction. Two modes: (A) Build — design a multi-platform ad strategy from scratch, (B) Optimize — audit existing cross-platform campaigns and reallocate budget. Works for Shopify, WooCommerce, standalone stores, and marketplace sellers expanding to external traffic. No API key required.

Create video marketing strategy for e-commerce brands. Product videos, unboxing, tutorials, UGC, live streams, and platform-specific video optimization for Amazon, TikTok, YouTube, and Instagram.

E-commerce product description generator for any platform. Generates optimized titles, bullet points, descriptions, and backend keywords using competitor research + keyword scoring + FABE copywriting. Two modes: (A) Create — generate listing from product specs with optional competitor analysis, (B) Optimize — improve existing listing with keyword gap analysis. Supports Amazon, eBay, Walmart, Shopify, Etsy, TikTok Shop, Lazada, Shopee. No API key required. Use when: (1) writing a new product listing, (2) analyzing what makes competitors rank, (3) improving an underperforming listing.

Run data-driven A/B tests on your Shopify store. Test product pages, pricing, images, copy, checkout flow, and marketing campaigns with proper statistical methodology.

Shopify Markets — multi-currency, translation, duties/taxes, localized pricing, market-specific content

High-converting landing pages — campaign pages, collection pages, seasonal promos, A/B testing

Complete marketing strategy for Shopify stores. SEO, email marketing, paid ads, social media, conversion optimization, and retention tactics specifically tailored for Shopify/DTC brands.

AI-powered synthetic monitoring skill for e-commerce websites. Designs automated user journey tests for add-to-cart, checkout, and payment flows with alerting rules and performance baselines.

AI-powered visual regression testing skill for e-commerce websites. Designs screenshot comparison workflows, mobile/desktop visual checks, and change detection alerts to prevent conversion-killing UI

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Use when the user wants crawl coverage, platform detection, dataLayer discovery, or a fresh artifact directory before grouping and schema work.

Use when the user wants to inspect the real live GTM runtime before schema generation or compare multiple live GTM containers.

Use when the platform is Shopify or the run needs the Shopify-specific schema, sync, install, or verification branch.

Self-contained test automation — invoke directly, do not decompose. End-to-end integration test that assembles a fixture, deploys to Cloudflare (with auto-provisioned Connect), and presents a live URL for browser verification. Use when testing the plugin, running E2E tests, verifying deployment works, or checking that templates assemble correctly.

Creates visual concepts for album artwork and generates AI art prompts. Use during planning for concept discussion, or after all tracks are Final for actual artwork generation.

Shows a structured progress dashboard for an album with percentage complete per phase, blocking items, and status breakdown. Use for a quick visual overview of album progress.

Scans lyrics for phrases that may match existing songs using web search and LLM knowledge. Use before release to check for unintentional borrowing.

**Input**: $ARGUMENTS

Generates platform-specific social media copy from album themes, track concepts, and lyrics. Use when promo/ templates need to be populated before release.

Scans lyrics for pronunciation risks and prevents Suno mispronunciations. Use when writing lyrics with proper nouns, technical terms, homographs, or non-English words.

Runs automated tests to validate plugin integrity across 14 categories. Use before creating PRs, after making changes to skills or templates, or to verify plugin health.

Use when running claudikins-kernel:verify, checking implementation quality, deciding pass/fail verdicts, or enforcing cross-command gates — requires actual evidence of code working, not just passing tests

Build a reproducible, cached environment overlay for ephemeral containers using a Dockerfile-like spec.

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Augmented vision tools for analyzing images beyond native visual capabilities. Use when tasked with describing images in detail, reproducing images as SVGs, identifying subtle features, comparing image regions, reading degraded text, or any task requiring careful visual inspection. Also use when the image-to-svg skill needs ground truth about colors, shapes, or boundaries.

Write effective instructions for Claude: project instructions, standalone prompts, and skill content. Use when users need help writing prompts, setting up project instructions, choosing between instruction formats, or improving how they communicate with Claude. Covers writing principles, model-aware calibration, and format selection. For building and testing complete skills, use skill-creator instead.

Systematic web application penetration testing methodology. Apply when performing authorized security assessments, bug bounty hunting, or pre-deployment security validation. Covers recon, scanning, exploitation, and reporting.

Build end-to-end tests with Playwright, Feature Object pattern, cross-browser testing, and visual regression. Apply when testing critical user flows, automating regression testing, or validating integrations.

Design database schemas, create migrations, manage data relationships, and sync with production using Prisma. Apply when designing database schemas, creating migrations, or defining data models.

Enforce strict Test-Driven Development with Red-Green-Refactor discipline. Apply when implementing new features, fixing bugs, or refactoring code. Ensures tests are written before implementation.

Apply TDD with RED-GREEN-REFACTOR cycles, separate unit tests from integration tests, ensure comprehensive coverage. Apply when writing tests, evaluating test coverage, testing databases, or testing admin flows.

Extract structured data from construction PDFs. Convert specifications, BOMs, schedules, and reports from PDF to Excel/CSV/JSON. Use OCR for scanned documents and pdfplumber for native PDFs.

Extract structured data from construction specifications. Parse CSI sections, requirements, submittals, and product data from spec documents.

Build automated BIM validation pipelines for IFC/Revit data. Continuous validation against IDS, LOD requirements, COBie, and project-specific BEP standards.

Check BIM data against IDS (Information Delivery Specification). Validate model information requirements and compliance.

Implement semantic vector search for construction data. Build AI-powered search using embeddings and vector databases (Qdrant, ChromaDB) for intelligent querying of specifications, standards, and project documents.

Build multi-agent AI systems for construction estimation. Use CrewAI/LangGraph to orchestrate specialized agents: QTO agent, pricing agent, validation agent. Automate complex estimation workflows.

Construction quality control workflow automation. Manage QC inspections, track defects, generate NCRs, and ensure specification compliance throughout the project.