디자인 스킬

Manage per-feature living documents that capture decisions, constraints, and reasoning across AI sessions during active development. Scoped to feature-level work — design, implementation, bugfix, refactor — not for codebase-wide assessments or product-wide specifications (those define their own document lifecycles). Handles creating new context documents, loading existing ones, and enriching them with new decisions. Use when starting a new feature, resuming work, making technical decisions, resolving questions, or when context needs to persist across sessions. Use this skill whenever the user mentions 'load context', 'update context', 'context doc', 'decisions', 'continue where we left off', 'what did we decide', or 'capture this decision'.

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Protocol for handling ambiguous decisions and missing/conflicting knowledge during code generation, design, and review. Ensures AI surfaces genuine judgment calls with structured options and stops on hallucination risk instead of silently assuming. Use when a decision has multiple valid approaches, when facts are missing or contradictory, when the user asks 'what should we do here?', 'is this a judgment call?', 'should I ask about this?', 'am I guessing here?', 'what are the tradeoffs?', or when deciding between two reasonable architectural or design options. Also composed by molecules to define how judgment calls and clarification requests are surfaced and resolved.

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Enforce architectural rules when generating or modifying code, and validate proposed designs before approval (design mode). Defaults to clean architecture; supports any architecture style via the architecture-refiner. Validates layer responsibilities, dependency direction, and structural constraints using the loaded architecture rules. Use when generating code, reviewing architecture, creating new files, or when the user mentions 'architecture', 'layers', 'structure', 'dependency rules', 'hexagonal architecture', 'ports and adapters', 'modular monolith', or 'onion architecture'. Also use when reviewing generated code for structural compliance.

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Exports publication-ready figures in various formats with proper resolution, sizing, and typography. Use when preparing figures for journal submission, creating vector graphics for presentations, or ensuring consistent figure styling across analyses.

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Predict B-cell and T-cell epitopes using BepiPred, IEDB tools, and structure-based methods for vaccine and antibody design. Identify immunogenic regions in antigens. Use when designing vaccines, mapping antibody binding sites, or predicting immunogenic peptides.

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Analyzes CRISPR drug-modifier (chemogenomic) screens with drugZ (Li & Hart 2019 Genome Med), a bidirectional Z-score method that identifies synthetic-lethal sensitizing genes and resistance-conferring suppressor genes from vehicle vs drug comparisons. Covers vehicle-anchored design (not Day-0), the bidirectional Z math giving 2-3x sensitivity over MAGeCK / STARS / edgeR / RIGER on drug screens, per-gene sumZ and normZ, synth (sensitizer) vs supp (suppressor) FDR, multi-dose handling, integration with control sgRNAs, and comparison with MAGeCK MLE with dose covariate. Use when running a drug-modifier CRISPR screen, identifying sensitizing or resistance genes for a drug candidate, choosing drugZ vs MAGeCK MLE for chemogenomic analysis, troubleshooting low-effect drug screens where MAGeCK lacks sensitivity, or designing a drug-screen layout (vehicle vs drug arms).

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Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.

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Designs covalent inhibitors and warheads targeting cysteine (most common, 98% of covalent drugs), lysine, serine, threonine, tyrosine, and aspartate residues, with explicit handling of warhead reactivity (acrylamide, chloroacetamide, vinyl sulfone, sulfonyl fluoride, fluorosulfate, aldehyde, boronate, nitrile), reversibility (kinact/Ki, t_residence), glutathione (GSH) stability, intrinsic reactivity assays, and covalent docking (DOCKovalent, GOLD, HCovDock). Use when designing covalent inhibitors for targeted covalent inhibition (TCI), KRAS G12C-style approaches, or rationalizing covalent SAR.

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Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups, eggNOG-mapper, JustOrthologs, and TOGA whole-genome-alignment orthology. Use when building single-copy ortholog sets for phylogenomics, classifying co-orthologs and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.

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Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo, mCross (CL-position-registered motifs), PEKA (positional k-mer enrichment), RBPamp (affinity), and RNA Bind-n-Seq (RBNS) cross-validation. Use when characterizing RBP sequence specificity, registering motifs to crosslink positions, validating in vivo CLIP motifs against in vitro RBNS Kd, reconciling motif disagreements across tools, or correcting for the uracil crosslinking bias that contaminates raw CLIP motif logos.

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Designs experiments to minimize and account for batch effects using balanced layouts and blocking strategies. Use when planning multi-batch experiments, assigning samples to sequencing lanes, or designing studies where technical variation could confound biological signals.

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Analyzes base-editing screens for variant function. Covers library design (Sanson 2020 GRACE, Hanna 2021 BRCA1/2 SNV scanning, Cuella-Martin 2021), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end, wider for ABE8e), bystander-edit quantification and the variant-call ambiguity it creates, sgRNA-efficiency filtering before hit calling, indel byproduct interpretation, the substitution-vs-indel diagnostic, variant annotation against ClinVar / COSMIC, and the Broad be-validation-pipeline. Use when designing a BE variant screen, choosing CBE vs ABE for a specific edit, interpreting bystander-confounded hits, distinguishing functional signal from indel artifact, integrating CRISPResso2 output with screen scoring, or deciding BE vs PE for SNV installation.

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Design guides for cytosine and adenine base editing using editing window optimization and BE-Hive outcome prediction. Select optimal positions for C-to-T or A-to-G conversions without double-strand breaks. Use when designing base editor experiments for precise nucleotide changes.

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Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and the model-based alternative of including batch as a covariate in MAGeCK MLE or Chronos. Covers screen-specific batch sources (passage cohort, library lot, infection day, sequencing run, Cas9 lot, FBS lot), PCA + variance-decomposition diagnostic to decide if correction is needed, when correction harms biology by over-correcting condition into batch, limma removeBatchEffect for visualization-only correction, and relationship to multi-condition design matrices. Use when combining screens for joint analysis, when passage cohort confounds biology, when DepMap-style panels need Chronos with batch covariates, when picking ComBat vs RUV, or when correction harms biology and should be replaced with explicit covariate modeling.

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Analyze DNA/RNA/protein sequences. Use when the user provides a sequence and asks for analysis, translation, GC content, ORFs, motifs, restriction sites, or primer design. Triggers on "sequence", "translate", "GC content", "ORF", "primer", "restriction", "complement", "reverse complement".

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Bulk transcriptomics differential expression with count-aware modeling, design validation, contrast handling, thresholded exports, and publication-ready DE figures.

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Proteina-Complexa flow-based protein backbone generation with fold-conditioned sampling guidance. Use this skill when: (1) Generating de novo protein backbones with hierarchical fold conditioning, (2) Exploring long-chain backbone generation beyond standard diffusion baselines, (3) Using NVIDIA Proteina-style flow matching workflows for controllable backbone design, (4) Comparing flow-based backbone generation against RFdiffusion or BoltzGen, (5) Prototyping fold-guided backbone campaigns before sequence design. This skill is based on the public NVIDIA Digital Bio Proteina project and uses "Proteina-Complexa" as the BioClaw-facing skill label. For sequence design after backbone generation, use proteinmpnn or solublempnn. For QC thresholds, use protein-design-qc.

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Protein design quality control, filtering thresholds, and ranking guidance. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines, deamidation, polybasic clusters), (4) Creating multi-stage filtering pipelines, (5) Computing PyRosetta interface metrics (dG, SC, dSASA), (6) Checking biophysical properties (instability, GRAVY, pI), (7) Ranking designs with composite scoring. This skill provides research-backed thresholds from binder design competitions and published benchmarks.

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Fetch and analyze protein structures from RCSB PDB. Use this skill when: (1) Need to download a structure by PDB ID, (2) Search for similar structures, (3) Prepare target for binder design, (4) Extract specific chains or domains, (5) Get structure metadata. For sequence lookup, use uniprot. For binder design workflow, use binder-design.

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Structure prediction using Boltz-1/Boltz-2, an open biomolecular structure predictor. Use this skill when: (1) Predicting protein complex structures, (2) Validating designed binders, (3) Need open-source alternative to AF2, (4) Predicting protein-ligand complexes, (5) Using local GPU resources. For QC thresholds, use protein-qc. For AlphaFold2 prediction, use alphafold. For Chai prediction, use chai.

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Structure prediction using Chai-1, a foundation model for molecular structure. Use this skill when: (1) Predicting protein-protein complex structures, (2) Validating designed binders, (3) Predicting protein-ligand complexes, (4) Using the Chai API for high-throughput prediction, (5) Need an alternative to AlphaFold2. For QC thresholds, use protein-qc. For AlphaFold2 prediction, use alphafold. For ESM-based analysis, use esm.

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Ligand-aware protein sequence design using LigandMPNN. Use this skill when: (1) Designing sequences around small molecules, (2) Enzyme active site design, (3) Ligand binding pocket optimization, (4) Metal coordination site design, (5) Cofactor binding proteins. For standard protein design, use proteinmpnn. For solubility optimization, use solublempnn.

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End-to-end protein design pipeline guide across preparation, generation, validation, and filtering. Use this skill when: (1) Starting a new protein design project, (2) Need step-by-step workflow guidance, (3) Understanding the full design pipeline, (4) Planning compute resources and timelines, (5) Integrating multiple design tools. For tool selection, use binder-design-tool-selection. For QC thresholds, use protein-design-qc.

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Discover and invoke 1,676 deduplicated biomedical AI agent skills from the Awesome Bio Agent Skills repository (20 source repos, 15 categories). Use this skill as a router whenever a user needs a bioinformatics/biomedical task (genomics, transcriptomics, single-cell, proteomics, protein design, clinical, epigenomics, multi-omics, pathway, metagenomics, database queries, visualization, workflows): search the index, locate the best-matching skill, fetch its SKILL.md, and follow it.

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