organon

Draft manuscript sections, format citations, and get AI peer review. Natural language invocation -- describe what you need and the skill routes to drafting, citation formatting, or peer review. Reads research profile, data analysis outputs, and literature search results for context-aware writing. After drafting, offers to generate supporting figures via viz skills. Triggers on: "draft introduction", "write methods", "format citations", "APA style", "bibliography", "peer review", "review my draft", "write abstract". Does NOT trigger for: literature search (use sci-literature-research), data analysis (use sci-data-analysis), image generation (use viz-nano-banana), repurpose/blog/lay summary (use sci-communication).

Transfer the visual style of a reference paper figure onto the user's own data. Takes a screenshot of a figure from a paper plus tabular data and produces an editable matplotlib script in that figure's register, gated by a mechanical quality floor and a Drawer/Reviewer refinement loop. Output is a self-contained .py + PNG + Type-42 PDF. Triggers on: "match this figure style", "figure in the style of", "make my plot look like this paper", "publication figure from reference", "style transfer figure", "reproduce this figure with my data", "NeurIPS-quality version of this chart". Does NOT trigger for: plain data plots with no reference image (use sci-data-analysis), AI-generated illustrations (use viz-nano-banana), flowcharts/architecture/sequence diagrams (use viz-diagram-code), hand-drawn sketches (use viz-excalidraw-diagram).

Publish and edit markdown blog posts on Substack as drafts — converts markdown to Substack's ProseMirror schema, uploads local images to Substack's CDN, pre-renders mermaid diagrams to PNG, and creates or updates drafts via Substack's private API. Draft-only by design — publish is always a human click. Triggers on: "push to substack", "substack draft", "publish to substack", "create substack draft", "send to substack", "substack this post", "update substack", "edit substack draft", "list substack drafts". Does NOT trigger for: reading existing Substack posts, subscriber management, newsletter scheduling. Does NOT publish — only creates/updates drafts you review and publish by hand.

Create new skills, modify and improve existing skills, and measure skill performance. Use when users want to create a skill from scratch, edit, or optimize an existing skill, run evals to test a skill, benchmark skill performance with variance analysis, or optimize a skill's description for better triggering accuracy.

End-of-session checklist that reviews deliverables, collects feedback, fixes skills, updates learnings, and commits work. Use when the user says "wrap up", "close session", "end session", "wrap things up", "we're done", "that's it for today", "session done", or invokes /wrap-up. Run at the end of any working session or after completing a major deliverable. Does NOT trigger for content writing, voice extraction, positioning, or audience research.

Schedule recurring tasks that run automatically via a system-level watchdog, even when Claude Code is closed. Job definitions persist in cron/jobs/ as the registry. The watchdog (launchd on Mac, Task Scheduler on Windows) checks every hour and runs due jobs headlessly via claude -p. Triggers on: "schedule a job", "cron job", "run this every morning", "automate daily", "recurring task", "set up a scheduled job", "check scheduled jobs", "list scheduled jobs", "install watchdog", "uninstall watchdog". Does NOT trigger for one-off tasks or in-session reminders.

Parallel-tempering simulated annealing for rugged multi-modal landscapes where local SA stalls. N replicas at a geometric temperature ladder with periodic adjacent-pair exchanges (Metropolis-Hastings). Contribution-weighted coordinate sampling + O(n) incremental delta evaluators. Triggers: "parallel tempering", "simulated annealing", "PT-SA", "replica exchange", "temperature ladder", "MCMC optimization". Not for: gradient descent, convex optimization, linear programming.

Discrete float64 ULP coordinate-descent polisher for high-precision optimization. Per-coordinate +/-1/2/4 ulp trials priority-ordered by contribution-weighted badness. Use when gradient methods stall at ~1e-12 but true residual is ~1e-13 (spherical codes, kissing configs, lattice packings). Triggers: "ulp polish", "polish to zero", "precision polish", "bridge precision floor", "float64 coordinate descent", "break through 1e-13".

Create science outreach content -- blog posts, tutorials, concept explainers, lay summaries, newsletters, social threads, and press releases from any source. Accepts papers, concepts, URLs, datasets, or personal expertise as input. Includes visual generation for inline diagrams and illustrations. Triggers on: "blog post", "tutorial", "explain this concept", "lay summary", "science blog", "write a tutorial about", "newsletter", "social thread", "press release", "explain for non-scientists", "teach this", "gentle introduction", "explainer", "educational content", "science communication", "scicomm". Does NOT trigger for: manuscript drafting (use sci-writing), literature search (use sci-literature-research), data analysis (use sci-data-analysis).

Three-persona mathematical research fan-out. Asks Gauss (algebraic / number-theoretic), Erdős (probabilistic / extremal), and Tao (harmonic / arithmetic-combinatorics) the same problem independently in parallel, then synthesises their 3×3 proposals into one ranked table with cross-persona consensus flags and composite scores. Use when a hard math problem needs breadth — stuck competitions, Einstein Arena openings, a new research question where a single frame is likely to miss something. Triggers "research council", "ask the council", "mathematician council", "3 personas", "gauss erdos tao", "fan out personas", "research fan-out". Does NOT trigger for literature search (use sci-literature-research) or single-author scientific writing (use sci-writing).

Load, analyze, clean, and visualize scientific data. Natural language invocation -- describe what you need and the skill routes to the right operation. Supports CSV, Excel, JSON loading with profiling. Statistical tests (t-test, ANOVA, chi-square, correlation, regression) with assumption checking. Data cleaning (missing values, outliers, normalization). Dual output plots: publication-quality Matplotlib + interactive Plotly HTML. Triggers on: "load data", "analyze", "statistics", "t-test", "ANOVA", "correlation", "regression", "clean data", "plot", "chart", "graph", "scatter", "histogram", "box plot", "heatmap", "visualize". Does NOT trigger for: literature search, paper writing, hypothesis generation, explaining data patterns (use sci-hypothesis), group differences interpretation (use sci-hypothesis), AI image generation (use viz-nano-banana).

Generate testable hypotheses from data patterns and literature, design experiments with power analysis and sample size calculations, and validate hypotheses with statistical tests on an evidence spectrum. Natural language invocation -- describe your research question and the skill routes to generate, design, or validate mode. Reads research profile for field personalization. Triggers on: "hypothesis", "generate hypothesis", "what could explain", "experiment design", "design experiment", "protocol", "sample size", "power analysis", "validate hypothesis", "test hypothesis", "evidence for", "support or reject", "group differences", "data shows", "treatment vs control", "observed pattern", "differential expression", "what is driving", "what explains", "data pattern", "I noticed", "my data suggests". Does NOT trigger for: data analysis (use sci-data-analysis), literature search (use sci-literature-research), writing (use sci-writing).

Search, summarize, cite, and analyze trends in scientific literature. Federated search across PubMed, arXiv, OpenAlex, and Semantic Scholar via the paper-search MCP server. AI-powered paper summaries personalized to your research profile. BibTeX citation export with AuthorYear keys. Trend analysis showing emerging research areas with evidence. Unified trend analysis combining publication surges with social/web signals (Reddit, X, web) via sci-trending-research integration. Scope options: publications, social, or combined. Triggers on: "search papers", "find papers", "literature search", "paper summary", "summarize paper", "cite", "bibtex", "export citation", "publication surge", "unified trends", "combined trends", "social trends", "publication trends", "parallel fanout", "fan out search", "concurrent literature search". Does NOT trigger for: data analysis, writing, hypothesis generation.

Catalog of named optimisation recipes with trigger-based dispatch. Each recipe covers a distinct pattern (Dinkelbach for fractional programs, k-climbing for deceptive landscapes, Remez exchange for minimax polynomial, cross-resolution basin transfer, square parameterisation, ULP descent, mpmath precision lottery, LP reformulation, Nelder-Mead / L-BFGS fallbacks, sigmoid bounding, incremental O(n) loss) with trigger conditions, pseudocode, worked example, gotchas, and citations. Router matches the user's problem description against recipe keywords and returns the best fit. Use when you want a principled pattern before reaching for ad-hoc code. Triggers "optimization recipe", "recipe for", "dinkelbach", "variable neighborhood", "remez exchange", "cross-resolution transfer", "ulp descent", "lp reformulation", "mpmath lottery", "sigmoid bounding", "incremental loss". Does NOT trigger for literature search, data analysis, or writing.

Mathematical optimization toolkit for competition math. LP solving, column generation, cutting-plane methods, ULP float64 polishing, and intelligent variable selection. Problem-agnostic primitives for Einstein Arena and similar platforms.

Capture research notes, track projects with milestones and deadlines, schedule automated science tasks, and run cross-skill pipelines. Four modes via natural language: note (capture, search, promote), project (create, dashboard, detail, update), schedule (presets, custom, list), pipeline (run, create, list). Triggers on: "research note", "log observation", "jot down", "capture idea", "research project", "track project", "milestones", "deadlines", "project dashboard", "schedule alerts", "paper alerts", "set up monitoring", "deadline reminders", "run pipeline", "literature monitor", "data watch", "search notes", "promote experiment". Does NOT trigger for: data analysis (use sci-data-analysis), literature search (use sci-literature-research), hypothesis generation (use sci-hypothesis), scientific writing (use sci-writing).

Build and manage a scientist's research profile via interactive onboarding. Captures core identity, research focus, preferences, and tool ecosystem. Stored in research_context/research-profile.md for downstream skills. Triggers on: "research profile", "set up my profile", "who am I", "my research", "update profile", "research onboarding", "configure research". Foundation skill -- run before any execution skill that reads research context. Does NOT trigger for literature search, data analysis, or manuscript writing.

Browse and search the Harvard ToolUniverse catalog of 2,200+ biomedical tools from the CLI, and create custom scientific skills with validated templates. Two modes: browse (search, filter, drill-down on biomedical tools) and create (generate sci-* skills from natural language descriptions with scientific defaults). Triggers on: "tools for", "find tools", "search tools", "browse tools", "ToolUniverse", "biomedical tools", "what tools exist for", "tool catalog", "refresh tools", "update catalog", "create a research skill", "build a science skill", "new scientific skill", "custom research skill". Does NOT trigger for: general "create a skill" without science context (use meta-skill-creator), data analysis (use sci-data-analysis), literature search (use sci-literature-research).

Research what's trending in science — emerging topics, publication surges, community discussions on academic Reddit (r/science, r/bioinformatics, r/MachineLearning, etc.), science Twitter/X, preprint servers, and the web. Surface real discussions, breakthroughs, and debates scientists are talking about right now. Produces a research brief other sci-* skills can consume. Triggers on: "what's trending in", "emerging research", "hot topics in", "recent breakthroughs", "what are researchers saying about", "field pulse", "research trends", "community sentiment on". Does NOT trigger for literature search (use sci-literature-research), data analysis, or manuscript writing.

Autonomous end-to-end attack pipeline for any Einstein Arena problem. Composes recon -- parallel 5-agent research spawn -- hypothesis graph synthesis -- OVERVIEW.md -- user gate -- attack -- polish -- tri-verify -- submit gate -- retrospective. Triggers on "attack arena problem", "investigate arena challenge", "work on challenge", "new arena problem", "autonomous arena attack", "bootstrap arena attack", "arena investigate", "attack this problem". Not for tactical polish only (use tool-arena-runner) or raw API ops (use tool-einstein-arena).

Single entry point for Einstein Arena campaigns. Eight subcommands -- precision ops (polish, tri-verify, recon) and API ops (fetch, register, analyze, submit, monitor). Composes ops-ulp-polish and tool-einstein-arena scripts into one CLI. Triggers: "arena runner", "arena polish", "tri-verify", "arena recon", "bootstrap arena", "three-method verification", "verify solution three ways", "einstein arena", "arena problem", "submit to arena", "check leaderboard", "register agent", "fetch problem", "analyze competitors". Not for: general optimization (sci-optimization).

Compete on Einstein Arena — register agents, fetch problems, analyze competitors, submit solutions, and monitor evaluations across all 18 math competition problems at einsteinarena.com.

Convert websites into LLM-ready data with Firecrawl API. Scrape, crawl, map, search, extract, agent, batch, change tracking, and branding extraction. Handles JavaScript rendering, anti-bot bypass, PDF/DOCX parsing. Requires FIRECRAWL_API_KEY in .env. Used by other skills (sci-communication, sci-trending-research) as a scraping backend when default web tools fail. Use when: scraping websites, crawling sites, web search + scrape, autonomous data gathering, monitoring content changes, extracting structured data. Does NOT trigger for general browsing or simple URL fetching that WebFetch can handle.

Stage Organon deliverables into Google Drive via the desktop app's local sync folder. Zero OAuth, zero API keys — files copied into the sync folder upload automatically. Auto-categorizes by extension (data, figures, manuscripts, presentations, papers, notes). Use when: "push to Drive", "upload to Google Drive", "sync this to Drive", "share this file", "stage output for collaborators", "backup to Drive". Does NOT trigger for Google Docs/Sheets programmatic editing — that needs a separate API-based skill. Requires Google Drive desktop app installed and signed in.

Remove AI-generated writing patterns and restore natural human voice. Detects and fixes 50+ AI tells: inflated symbolism, promotional language, hedging, corporate buzzwords, robotic structure, em dash overuse, rule of three, vague attributions, negative parallelisms, conjunctive phrase abuse. Three modes: quick (obvious patterns), standard (full scan + score), deep (voice-matched using research_context/research-profile.md). Called automatically by sci-communication as a post-processing step for blog posts, social threads, and newsletters. Also invoked standalone: "humanize this", "de-AI this", "make this sound human", "remove AI patterns", "clean up this writing". Does NOT trigger for formal academic writing (sci-writing handles that). Does NOT trigger for content that is intentionally formal or academic.

Optional knowledge-base integration. Writes well-formed markdown notes (with YAML frontmatter, tags, and [[wikilinks]]) into a local Obsidian vault so the user's graph picks them up. Zero plugins required — filesystem-only passthrough. Categories: data-notes, paper-notes, daily, experiments, drafts, inbox. Auto-detects vault via OBSIDIAN_VAULT env var, Obsidian's vault registry, or common paths. Use when: "save to obsidian", "add to vault", "log to daily note", "capture to inbox", "search my notes", "open in obsidian". Does NOT trigger for Organon's own context/memory/ — that stays local. Skill is OPTIONAL — framework works without Obsidian installed.

Search and read 8M+ biomedical papers from bioRxiv, medRxiv, and PubMed Central using the paperclip CLI.

Fetch latest videos from YouTube channels and extract full transcripts. Two modes: channel mode (list recent uploads, needs YOUTUBE_API_KEY) and transcript mode (get full timestamped transcript from a URL, free via yt-dlp). Chain both to get the latest video's full transcript from any channel. Triggers on: "latest youtube video", "get transcript", "youtube transcript", "what did they post", "fetch from youtube", "channel updates". Used by other skills (sci-communication, sci-trending-research) as a content source. Does NOT trigger for content creation, repurposing, or video editing.

Generate polished diagrams from code using Mermaid -- flowcharts, sequence diagrams, architecture diagrams, mind maps, timelines, class diagrams, and comparison layouts. Produces SVG + PNG with precise text, professional styling, and color themes. Ideal for blog posts, tutorials, and educational content where text accuracy matters. Triggers on: "mermaid diagram", "flowchart", "sequence diagram", "architecture diagram", "mind map diagram", "timeline diagram", "class diagram", "process diagram", "comparison diagram", "diagram with code", "styled diagram", "code diagram". Does NOT trigger for: hand-drawn/sketch diagrams (use viz-excalidraw-diagram), AI-generated illustrations (use viz-nano-banana), data plots (use sci-data-analysis).

Generate Excalidraw diagram JSON files that make visual arguments — not just labelled boxes. Workflows, architectures, concepts, protocols, system designs. Triggers on: "excalidraw diagram", "draw a diagram", "visualize this workflow", "hand-drawn architecture", "system diagram", "diagram this", "excalidraw", "create a diagram of". Builds section-by-section for large diagrams, renders to PNG via Playwright, and validates in a loop until the output is clean. Brand colors configurable via color-palette.md. Does NOT trigger for inline SVG diagrams (use graphics-diagram), charts/graphs, or slide decks.

Generate images, infographics, and visual content via Gemini 3 Pro Image. Six styles: technical, notebook, comic, color, mono, scientific. Direct prompt or SVG blueprint modes. Triggers on: "generate an image", "create an infographic", "nano banana", "notebook sketch", "comic strip", "hand-drawn diagram", "visual for", "make an image of", "sketchnote", "storyboard", "generate a visual", "image of", "draw me", "scientific illustration", "diagram", "experimental setup", "pathway", "cell diagram", "molecular mechanism", "scientific figure", "schematic". Image generation backend for all skills needing visuals. Does NOT trigger for Excalidraw diagrams, charts/graphs, slide decks, or text-only content.

Generate presentation slide decks from markdown using Marp. Convert blog posts, tutorials, manuscripts, academic PDFs, or topic descriptions into professional slides with math equations, code highlighting, extracted figures, diagrams, and speaker notes. Includes narrative-driven paper-to-slides mode using RST discourse analysis for academic talks. Outputs PDF, PPTX, and HTML. Triggers on: "presentation", "slide deck", "slides", "make a presentation", "convert to slides", "create slides about", "prepare a talk", "lecture slides", "conference presentation", "seminar presentation", "poster presentation", "paper to slides", "pitch deck", "turn this paper into a talk". Does NOT trigger for: diagrams only (use viz-diagram-code), illustrations (use viz-nano-banana), blog posts (use sci-communication).