Results for “structural-biology”

Use when studying cell biology.

Runs full Trailmark structural analysis by building a graph and computing pre-analysis passes for hotspots, taint, blast radius, privilege boundaries, and attack surface.

Teleological physiology analysis framework for understanding biological systems through multi-constraint optimization. Use when analyzing physiological mechanisms, explaining apparent biological "inefficiencies", preparing for medical examinations (CICM/ANZCA Primary), understanding why biological systems are designed the way they are, or when seeking deeper mechanistic understanding beyond descriptive knowledge. Triggers on questions like "why is X designed this way", "what purpose does Y serve", "how is Z optimized", analysis of physiological trade-offs, or exploration of evolutionary/design constraints.

Structural editor that proposes cuts, reorganization, and simplification while preserving comprehension. Use when user requests structural review or editorial review of structure

Applied Botany Analysis Skill

Explore codebases efficiently using AST-based structural search, outline, and symbol unfolding to reduce token usage.

Diagnose your own behavior by reading the structured logs you leave behind — turns.jsonl, events.jsonl, chat_history.jsonl, scheduler.yaml. Use when something has gone wrong (a message didn't land, a scheduled job isn't firing, a communication pattern feels off), when you need to understand a pattern over many turns, or when cost / token usage needs auditing. Covers jq query recipes and points at the debugging-jobs / debugging-communication / debugging-drift companion guides for specific failure modes.

Atomic-design guidance for Organisms — complex feature-level sections (Header, ProductGrid, CommentSection) that compose molecules, connect to state, handle loading/error/empty states, and own responsive layout decisions. Use when authoring components under ui/organisms or deciding molecule vs organism boundaries.

Botany Based Simulation Skill

Structured brainstorming for projects and features. Explores multiple options before implementation.

Use when performing pairwise structural alignments of RNA sequences that incorporate both sequence and structure information through base pair propensity vectors.

Token-optimized structural code search using tree-sitter AST parsing. Use instead of reading full files when you need to understand code structure, find functions, or explore a codebase efficiently.

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

Perform constraint-based metabolic modeling with COBRApy: run FBA, FVA, gene knockouts, flux sampling, and manage SBML models for systems biology and metabolic engineering.

Evaluate scientific claims and evidence quality by assessing experimental design, identifying biases and confounders, and applying evidence grading frameworks like GRADE and Cochrane Risk of Bias.

Provides a reference for structuring an Expo Router app, including folder layout, configuration files, and essential dependencies.

Structural editor that proposes cuts, reorganization, and simplification while preserving comprehension. Use when user requests structural review or editorial review of structure

Botany Based Design Skill

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

Structural editor that proposes cuts, reorganization, and simplification while preserving comprehension. Use when user requests structural review or editorial review of structure

Designs high-performing team structures using organizational psychology AND creates new skills on-the-fly when team needs unmet expertise. Expert in team composition, personality balancing, collaboration ritual design, and skill creation for missing capabilities. Use for team design, role definition, skill gap identification. Activates on 'team building', 'team composition', 'skills needed', 'what skills'. NOT for general project management or solo work planning.

Use when evaluating the free energy (kcal/mol) of an RNA secondary structure, calculating co-folding energies for two RNA strands, or analyzing consensus structures from multiple sequence alignments.