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概要と使いどころ
ENA REST API for sequences, reads, assemblies, and annotations. Portal API search, Browser API retrieval (XML/FASTA/EMBL), file reports for FASTQ/BAM URLs, taxonomy, cross-refs. For multi-DB Python use bioservices; for NCBI-only use pubmed-database or Biopython Entrez.
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KEGG REST API (academic only). Pathways, genes, compounds, enzymes, diseases, drugs via 7 ops (info/list/find/get/conv/link/ddi). ID conversion (NCBI/UniProt/PubChem). Use bioservices for multi-DB Python.
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Read, write, and edit ChemDraw CDX/CDXML files with RDKit's rdkit.Chem.rdChemDraw plus direct XML editing, always paired with a rendered PNG. Parse molecules and reactions from .cdxml/.cdx, write structures with good 2D depiction, and hand-build or modify the parts RDKit cannot write: reaction arrows, plus signs, schemes/steps, and text/labels. Use for reaction schemes, synthesis routes, mechanisms, retrosynthesis, or SI figures. Critical: RDKit writes structures only — round-tripping a reaction through a Mol silently drops arrows and text; this skill shows the XML layer that preserves them. For pure molecular analysis (descriptors, fingerprints, SMARTS) use rdkit-cheminformatics; for multi-format 3D conversion use openbabel.
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Deep learning for drug discovery. 60+ models (GCN, GAT, AttentiveFP, MPNN, ChemBERTa, GROVER), 50+ featurizers, MoleculeNet benchmarks, HPO, transfer learning. Unified load-featurize-split-train-evaluate API. For fingerprints use rdkit-cheminformatics; for featurization-only use molfeat.
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smina molecular docking CLI. AutoDock Vina fork with customizable scoring functions, native SDF/MOL2/PDB ligand input, autoboxing, local energy minimization, and per-atom score breakdowns. Pipeline: receptor PDBQT prep -> ligand prep (RDKit/OpenBabel) -> dock via autobox or explicit grid -> rescore/minimize with custom scoring -> rank poses by affinity. Choose smina over Vina when you need custom scoring terms (--custom_scoring), local optimization of an existing pose (--local_only), per-atom contributions (--atom_term_data), or SDF/MOL2 ligands without manual PDBQT conversion. For unknown binding sites use diffdock; for the Python-bindings/Vinardo workflow use autodock-vina-docking.
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Query RCSB PDB (200K+ structures) via the public REST + GraphQL APIs with plain `requests` (no SDK). Search by text, attribute, sequence, or 3D structure similarity (Search API); retrieve metadata via GraphQL (Data API); download PDB/mmCIF from files.rcsb.org. For AlphaFold predictions use alphafold-database-access; for protein sequences only use uniprot-protein-database.
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Cross-reference compound IDs across 20+ databases (ChEMBL, DrugBank, PubChem, ChEBI, PDB, SureChEMBL, HMDB, DrugCentral, BindingDB) via UniChem REST API. Resolve InChIKeys to source IDs, translate between source-specific IDs, find structurally related compounds by connectivity. POST with a JSON body for all cross-reference queries; only /sources is GET. No auth required.
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PNAS figure preparation: resolution (300-1000 PPI), formats (TIFF/EPS/PDF), strict RGB-only color, Arial/Helvetica fonts, italicized uppercase panel labels, automated image screening.
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scikit-learn compatible Python toolkit for time series ML: classify, cluster, regress, segment, transform with 30+ algorithms (ROCKET, InceptionTime, KNN-DTW, HIVE-COTE, WEASEL). Handles panel, multivariate, and unequal-length series. Maintained successor to sktime. Alternatives: sktime (larger ecosystem), tslearn (fewer algorithms), catch22 (features only).
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Python toolkit for neurophysiological signal processing: ECG (HR, HRV, R-peaks), EEG (complexity, PSD), EMG (activation onset), EDA/GSR (SCR decomposition), PPG, and RSP. Includes synthetic signal simulation. Alternatives: BioSPPy (less maintained), MNE (EEG/MEG specialist), heartpy (ECG only), scipy.signal (raw DSP).
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Scaffold a new SciAgent-Skills entry. Picks pipeline/toolkit/database/guide template, creates skills/{category}/{name}/SKILL.md with valid frontmatter, appends the registry.yaml entry, runs validation. Enforces name uniqueness, kebab-case, description keyword rules, schema rules from AGENTS.md. TRIGGER when user says (any language): "add a SciAgent skill", "add a skill for <X>", "create new skill", "create a SKILL.md for <X>", "scaffold a skill", "new skill entry", "register a skill", "신규 skill 추가", "스킬 만들어줘", "스킬 생성", "skill 만들어", or any request to add a new SKILL.md to this repo. ALWAYS invoke this skill BEFORE writing to skills/ or registry.yaml. DO NOT TRIGGER when: editing existing entry's content (just edit the file directly); migrating an existing entry (read AGENTS.md "Migrating from Existing Entries" first); only updating registry.yaml without creating a new SKILL.md.
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omics-plotting: publication-style figure authoring for omics / bioinformatics results with matplotlib / seaborn. Read this before writing any plotting or figure code in any omics analysis — RNA-seq, proteomics, single-cell, variant, or database results — not only when a plot is explicitly requested: whenever an analysis will produce a figure, load this first and follow its recipes. Covers volcano, MA, expression / correlation heatmap, GSEA bar / dot plot, box / violin / bar / ridgeline, PCA / UMAP / t-SNE scatter, Kaplan–Meier, Manhattan / QQ / forest. Supplies a shared journal-ready style and copy-paste recipes so every figure looks like one consistent system. To combine several plots into ONE multi-panel composite figure, use the sibling `multipanel` skill.
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Turn Chinese classical poems and ci into coherent vertical Chinese-art videos with poem-driven scene grouping, GPT ImageGen stills, Docker-only Gemini I2V, retained model-generated ambience, Gemini sparkle-watermark cleanup, brush-calligraphy captions revealed character by character, optional local BGM mixing, stitching, and final-frame QA. Supports verse-driven variation across ink landscape, gongbi bird-and-flower, colored figure-and-horse painting, blue-green landscape, xuan paper, silk, and related Chinese visual languages. Use when users ask for 古诗词动态视频、诗词逐句或两句一景、国风视频、毛笔字逐字出现、整首诗拼接成片，or want the established 月落乌啼霜满天 workflow applied to another poem.
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Persistent compounding memory for AI agents. 5 default MCP tools: session_start, session_end, remember, recall, check. Full surface: 6 tools with --full (adds check_action); 13 tools with AR_EXTRAS=1 --full. Two-verb model: inhale (session_start) and exhale (session_end). Correction-first memory with decision trail tracking, watch_for warnings, palace rooms with salience scoring, cross-project insight matching, same-day journal merging, ambient recall hooks. Local markdown only. Zero cloud, zero telemetry, Obsidian-compatible. Optional Supabase backend: when configured via `ar setup supabase`, recall() uses pgvector cosine similarity on OpenAI/Voyage embeddings instead of keyword search — same API, semantic understanding. Gracefully degrades to local search if not configured.
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Remove the discourse-level (structural) signs of AI writing that survive surface editing: stated lessons and moral-of-the-story closers, tidy single-track arcs, embodied-emotion performance ("chest tightened"), vague allusions instead of named references, unbroken linear structure, and shape convergence across pieces. Grounded in the StoryScope study (Russell et al. 2026): narrative structure alone detects AI text at 93.2% F1, and professional stylistic rewriting moved detection only 1.6 points. Use as the SECOND pass after the humanizer skill (which handles words and phrasing) whenever writing or revising LinkedIn posts, course lessons, blog posts, essays, newsletters, or emails that must read as human. Triggers: "humanize", "de-slop", "AI tells", "make this sound human", "structural pass", "deep humanize".
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Use when evaluating a newly adapted model's accuracy/eval score. Runs evalscope eval (or the test/srt/run_eval.py fallback) against an OpenAI-compatible endpoint on datasets like gsm8k / aime, producing per-dataset reports and a score. Accuracy only — throughput/latency benchmarks belong to model-speed-benchmark. Triggers on accuracy, eval, evalscope, gsm8k, aime, run_eval — not throughput.
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Use when running throughput/latency (serving speed) benchmarks against an already-running model server. Uses sgl_jax.bench_serving to sweep batch-size/concurrency and measure throughput and latency, producing summary.csv and per-point bs_<N>/result.jsonl. Speed only — accuracy/eval belongs to model-accuracy-benchmark. Triggers on throughput, latency, bench_serving, batch-size sweep, tok/s, TTFT, TPOT — not accuracy/eval.
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Evaluate WooAIAssistant against a structured scenario suite with hard invariants + LLM-as-judge rubric scoring. Runs live against the demo store + gpt-5.1 via the woo-mobile-ai backend wrapper, writes a JSONL run record, compares against stored baselines, and surfaces regressions. Always delegated to a subagent so the main context only sees the markdown report.
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Design, implement, audit, or review Shift user interfaces and shared UI components. Use for React components, Base UI primitives, Tailwind styling or theme tokens, Figma/reference matching, accessibility, icon-only actions, tooltips, menus, popovers, dialogs, forms, layout, and visible UI regressions.
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Serverless compute for Databricks jobs, Lakeflow pipelines and Declarative Automation Bundles (DABs), with STANDARD or PERFORMANCE_OPTIMIZED and classic only where serverless cannot run the workload. Use when creating, deploying, scheduling or editing a job or pipeline, or deciding its compute. Invoke BEFORE writing a job spec. For migrating existing classic workloads, use databricks-serverless-migration.
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Split an oversized skill, CLAUDE.md, or spec into an entry file plus files that load only when they're needed.
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Generate several genuinely different throwaway variations (designs, approaches, drafts) for the user to react to. Use when the user can only recognize what they want by seeing it — visual design, UX flows, naming, tone — or asks to brainstorm or prototype before building.
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Push records from apps, services, devices, or scripts directly into Unity Catalog Delta tables with Zerobus Ingest: SDKs (Python, TypeScript, Go, Java, Rust, C++, .NET), REST, OTLP, MQTT, Arrow Flight, or Apache Kafka-compatible producer APIs, with no message bus to run. Use to stream events, telemetry, logs, IoT data, CDC, or columnar batches into Databricks in near real time; connect existing collectors and log shippers (OpenTelemetry, Debezium, Vector, Telegraf, Cribl); replace a message bus that only feeds the lakehouse; or debug Zerobus auth, schema, throughput, or delivery issues.
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Analyze spreads, over/unders, prop bets. Historical trends, situational stats, value bet identification. For entertainment/education only.
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