Computational molecular biology library (sequence I/O, alignment, phylogenetics). Input: FASTA/GenBank/PDB files you already have. Output: parsed sequences, alignments, phylogenetic trees, structural analysis. Does NOT search databases — invoking by topic returns only a placeholder stub. For literature use pubmed, for protein lookup use uniprot, for sequence homology use blast.
Computational provenance audit verifying that every number, table, figure, ordering, and terminology in a manuscript is derived from code and scripts — not manually entered. Cross-references LaTeX source against the codebase to detect hardcoded values, stale outputs, broken pipelines, and manual data entry. Companion to manuscript-review: that skill audits the document as prose; this skill audits whether the document is faithfully generated from code. Use when the user says "check provenance", "verify reproducibility", "audit my pipeline", "are my numbers from code", "check manuscript against scripts", "provenance audit", or any request to verify that manuscript content traces back to computational outputs.
Systematic literature review workflow for surveying, synthesizing, and analyzing academic research. Covers the full lifecycle: scope definition, searching academic databases (arXiv, Semantic Scholar, Google Scholar), screening, structured extraction, thematic synthesis, gap identification, and producing a cited review document. Triggers on: "literature review", "survey the literature", "research landscape", "related work", "systematic review", "scoping review", "synthesize the research", "bibliography on", "find papers about", "review the state of the art", "research gap analysis". Use this skill when surveying a research area, mapping a topic landscape, identifying gaps, or writing a related work section.
Systematic pre-publication manuscript audit producing a structured refactoring report with section-level diagnostics, citation hygiene analysis, and submission-readiness assessment. Use this skill whenever the user uploads a manuscript, paper, thesis chapter, journal submission, or conference paper and asks for review, feedback, editing, refactoring, pre-submission check, proofreading, or quality audit. Also trigger when the user says "review my paper", "check before submission", "is this ready to submit", "pre-pub checklist", "manuscript review", "refactor my paper", or asks about citation consistency, argument coherence, or formatting compliance. Covers partial requests like "check my references" or "does the abstract work" — the full diagnostic surfaces issues across all facets even when only one was asked about.
Critical analysis of research papers, academic manuscripts, preprints, and technical studies — evaluating methodology, claims-evidence alignment, contribution significance, and intellectual honesty. Produces coherent analytical responses (not checklists) that distinguish genuine weaknesses from standard field limitations. Governs intellectual posture: collegial reader, not adversarial reviewer. Triggers on: "critique this paper", "review this research", "what do you think of this paper", "analyze this study", "evaluate the methodology", "is this paper sound", "assess this research", "strengths and weaknesses of this paper", "does the evidence support the claims". Use this skill when the user provides a research paper, preprint, or technical study and asks for critical evaluation of its scientific merit, methodology, or contribution — not formatting, citation hygiene, or submission readiness (use manuscript-review for those).
Update library documentation in .claude/docs/libraries/ with latest information from web search.
Research a library and create comprehensive documentation in .claude/docs/libraries/.
Review an MCP tool implementation for correctness, pattern adherence, and best practices. Use after implementing or modifying a tool.
Web search and content extraction via Kagi Search API. Use for searching documentation, facts, or any web content. Lightweight, no browser required.
Deep dive on a topic combining web search, papers, and synthesis
Find the one paper you should read today from Hugging Face Papers
Find and summarize new papers matching tracked research interests
Cross-platform social research — what people are actually saying about a topic across Reddit, X, HN, Polymarket, and the web over the last 30 days
Inventory active Aeon forks, detect diverged work, surface upstream contribution candidates
5 concrete real-life actions for today based on recent signals and memory
Search and analyze research papers, find related work, summarize key ideas. Use when user says "find papers", "related work", "literature review", "what does this paper say", or needs to understand academic papers.
AI paper reviewer. Use when the user says 'review my paper', 'help me review this paper', '审稿', 'give me feedback on my paper', 'check my manuscript', 'evaluate this paper for NeurIPS/ICLR/EuroSys'. Accepts PDF files and produces structured narrative reviews with venue-specific dimensional scores and Accept/Reject recommendation.
Detects CI/CD tools, containerization, and orchestration from public signals
Reviews chapter quality using 5 specialized checkers and generates comprehensive reports. Activates when user requests chapter review or /webnovel-review.
Plans detailed volume outlines with chapter-by-chapter breakdown, cool-point distribution, and Strand Weave pacing. Activates when user requests outline planning or /webnovel-plan.
Analyzes memory regions of a disassembled binary and converts them to the correct block types (code, bytes, words, text, tables, etc.) using MOS 6502 and the target platform's expertise.
Analyzes a sequence of memory containing Commodore BASIC tokens, formats address/word data types, and constructs side comments representing the plain BASIC commands.
Critiques ML conference papers with reviewer-style feedback. Use when users want to anticipate reviewer concerns, identify weaknesses, check claim-evidence gaps, or find missing citations.
Conduct a literature review and develop a CS research proposal. Use when asked to review a research area, find gaps in existing work, and propose a novel research contribution. The output is a research proposal identifying an assumption to challenge (the "bit flip") and how to validate it.
