Papers

ATRIS workspace navigation and task management. Use when user mentions atris, TODO, tasks, backlog, navigator, executor, validator, MAP.md, journal, inbox, or asks "where is X?" in an atris-enabled project.

Prepares Pine Scripts for publication in TradingView's community library with proper documentation and compliance. Use when preparing to publish, adding documentation, ensuring House Rules compliance, writing descriptions, or finalizing scripts for release. Triggers on "publish", "release", "documentation", "House Rules", or preparation requests.

Guide for using the AI's persistent journal database

Automated data visualization for EDA, model performance, and business reporting. Activates for "visualize data", "create plots", "EDA", "exploratory analysis", "confusion matrix", "ROC curve", "feature distribution", "correlation heatmap", "plot results", "dashboard". Generates publication-quality visualizations integrated with SpecWeave increments.

Multi-mode code quality analysis covering security reviews (OWASP Top 10), clarity refactoring (readability rules), and synthesis analysis (cross-file issues). Use when reviewing code for security vulnerabilities, improving code readability, conducting quality audits, pre-deployment checks, or when user mentions 'code quality', 'code review', 'security review', 'refactoring', 'code smell', 'OWASP', 'code clarity', or 'quality audit'.

Journelly-format journal entries. USE WHEN user wants to create journal entries, write reflections, or work with Journelly.org file.

Multi-LLM orchestration implementing the 5-stage coding workflow: Example Analysis → Hypothesis → Implementation → Debug Loop → Recursive Improvement. Based on "Towards a Science of Scaling Agent Systems" (Kim et al., 2025): - Centralized Consult architecture (Claude orchestrates, others advise) - Measured coordination (avoid MAS overhead in tool-heavy stages) - Tests-first selection (Poetiq pattern, not voting) Use when: Debugging complex issues, analyzing unfamiliar code, refactoring, or any task that benefits from diverse LLM perspectives with verification.

Guidance for building digital logic circuits that compute composite functions like Fibonacci of integer square root. This skill applies when implementing combinational and sequential logic in gate-level simulators, particularly when combining algorithms (like isqrt and Fibonacci) under resource constraints (gate counts, simulation steps). Use for circuit synthesis, HDL-style logic design, or gate-level algorithm implementation tasks.

Automate comprehensive market research using web data, competitive analysis, and structured synthesis. Use when researching markets, industries, competitors, or target audiences.

Guidance for designing and assembling multi-component fusion protein sequences, particularly for FRET biosensors and tagged constructs. This skill applies when tasks involve identifying proteins by spectral properties (excitation/emission wavelengths), assembling fusion proteins from multiple domains, codon optimization with GC content constraints, working with PDB sequences and fluorescent protein databases, or generating gBlock sequences for gene synthesis.

Synthesize competing positions through structured thesis-antithesis-synthesis process. Use when stakeholders disagree, trade-offs exist, or multiple valid perspectives need integration. Produces integrated positions with acknowledged trade-offs.

Performs quick research using web search and synthesis when user asks about unfamiliar topics, new technologies, or needs current information. Activates on questions like 'how does X work', 'what is Y', or when encountering unknown concepts. For deep comprehensive research, suggests knowledge-builder command.

Analyzes events through chemistry lens using molecular structure, reaction mechanisms, thermodynamics, kinetics, and analytical techniques (spectroscopy, chromatography, mass spectrometry). Provides insights on chemical processes, material properties, reaction pathways, synthesis, and analytical methods. Use when: Chemical reactions, material analysis, synthesis planning, process optimization, environmental chemistry. Evaluates: Molecular structure, reaction mechanisms, yield, selectivity, safety, environmental impact.

Analyzes events through journalistic lens using 5 Ws and H, investigative methods, source evaluation, fact-checking, newsworthiness criteria, and ethical journalism principles. Provides insights on story angles, information gaps, credibility, public interest, and media framing. Use when: Breaking news, information verification, source analysis, story development, media criticism. Evaluates: Factual accuracy, source credibility, completeness, newsworthiness, bias, public interest.

Use when user shares a Medium article URL behind a paywall and wants to read the full content. Also use for articles on Medium-hosted publications like towardsdatascience.com, betterprogramming.pub, levelup.gitconnected.com, etc.

Synthesize Reflector insights into structured delta proposals for playbook updates, following ACE paper's Curator architecture

Capture notes, logs, and journal entries to Thymer. Use when user says "note this", "log this", "capture this", "add to journal", "inbox this", "save this conversation", or wants to save content to their Thymer workspace.

Expert research analyst specializing in comprehensive information gathering, synthesis, and insight generation. Masters research methodologies, data analysis, and report creation with focus on delivering actionable intelligence that drives informed decision-making.

Systematic debugging with hypothesis-driven investigation. Use when something is broken, tests are failing, unexpected behavior occurs, or errors need investigation. Triggers on: "this is broken", "debug", "why is this failing", "unexpected error", "not working", "bug", "fix this issue", "investigate", "tests failing", "trace the error", "use debug mode". Full access mode - can run commands, add logging, and fix issues.

Looplia writer skill for generating content ideas with personalization. Reads user profile for context. Generates hooks, angles, and thought-provoking questions. Use after media-reviewer to transform analysis into creative content ideas.