Paperclip

Molecular docking prediction using DiffDock diffusion model

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DNA sequence profiling and genetic variant characterization

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Molecular data processing, featurization, and cheminformatics workflows

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Multi-perspective deliberation framework for complex scientific questions

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Constraint-based metabolic modeling and flux balance analysis

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Query ChEMBL bioactivity database for drug-like molecules

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Evidence-based clinical decision support and diagnostic reasoning

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Annotated data matrix operations for single-cell genomics using AnnData

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Self-update mechanism. Detects git vs vendored install. Auto-upgrade option with escalating snooze backoff. Syncs global and local copies. Extracts CHANGELOG bullets post-upgrade.

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Develops custom WordPress themes and plugins, creates Gutenberg blocks, configures WooCommerce stores, implements REST API endpoints, and applies security hardening.

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Gene regulatory network inference using tree-based ensemble methods

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Fully automated review pipeline: CEO, Design, and Eng reviews with auto-decisions using 6 principles (completeness, boil lakes, pragmatic, DRY, explicit over clever, bias toward action). Only pauses for premise confirmation. Classifies decisions as Mechanical (silent) or Taste (surfaced at final gate).

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Performance regression detection. Captures TTFB, FCP, LCP, bundle sizes, request counts. Regression thresholds: timing >50% or >500ms. Baseline comparison, trend tracking, budget compliance scorecard.

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Headless Chromium CLI for QA testing and site dogfooding. 100-200ms per command after startup. Persistent state with cookies, tabs, sessions. Snapshot system with element refs. Navigate, interact, verify page state, take screenshots, check responsive layouts, test forms, handle dialogs.

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Post-deploy monitoring. Watches live app via headless browser for console errors, performance regressions, page failures, visual anomalies. Alert on deltas not absolutes, transient tolerance (2+ consecutive checks). Default 10-minute monitoring window. Baseline capture mode.

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Multi-AI second opinion via OpenAI Codex CLI. Three modes: Review (pass/fail gate), Challenge (adversarial edge-case finder), Consult (freeform with session continuity). Read-only with streaming output and thinking traces. Cross-model analysis when review has already run.

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Build a complete design system from scratch. Competitive research via web search and browse. SAFE/RISK breakdown of choices. Self-contained HTML preview page. Outputs DESIGN.md as project design source of truth.

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Live-site visual QA audit with fix loop. 10-category checklist (~80 items) including AI Slop Detection (10 blacklisted patterns). Atomic commits per fix. Before/after screenshots. A-F grading. Parallel cross-model code-level design audit. Modes: Full, Quick, Deep, Diff-aware, Regression.

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Post-ship documentation sync. Updates README, ARCHITECTURE, CONTRIBUTING, CHANGELOG, TODOS, VERSION. Auto-applies factual corrections, asks for risky rewrites. CHANGELOG voice polish. Cross-doc consistency checks.

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YC Office Hours — product idea diagnostic before writing code. Two modes: Startup (6 forcing questions with rigorous pushback) and Builder (generative brainstorming). Outputs design doc. Includes landscape research, premise challenge, alternatives generation, visual wireframe sketching, and optional cross-model second opinion.

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CEO/founder-mode plan review. Four modes: scope expansion, selective expansion, hold scope, scope reduction. 10 review sections from architecture through long-term trajectory. Nuclear scope challenge, dream state mapping, error and rescue registry. Optional cross-model outside voice.

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Search and retrieve preprints from the arXiv repository

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Design critique with 7 rated passes: Information Architecture, Interaction State Coverage, User Journey and Emotional Arc, AI Slop Risk (10-item blacklist), Design System Alignment, Responsive and Accessibility, Unresolved Decisions. Each rated 0-10 with gap-fill loop. Parallel cross-model design voices.

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Eng manager-mode plan review. Scope challenge, architecture review, code quality review, detailed test coverage diagram, performance review. Produces test plan artifact for downstream QA. Optional cross-model outside voice.

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