scholaraio

Use when the user wants to install, configure, diagnose, or troubleshoot ScholarAIO, including setup check, dependency status, API keys, and bilingual setup flow.

Use when the user explicitly asks for Nature Skills, nature-skills, Nature style, Nature-style, Nature Communications, Nature-family, CNS, high-impact journal, or Springer Nature workflows, including Nature figure work, polishing, writing, reviewer critique, high-impact journal major revision response, Nature/CNS citations, Nature data-sharing workflows, paper readers, reviewer response, paper-to-PPT, submission checklist, or Nature-specific academic-search workflows.

Use when the user wants to rebuild or refresh ScholarAIO keyword, full-text, FTS5, FAISS, or semantic search indexes after data or metadata changes.

Use when the user wants to find academic papers, search the local library, run keyword or semantic search, search by author, explore topics, or federate across library, explore databases, and arXiv.

Use when the user wants to import papers from Endnote XML/RIS, Zotero Web API or local SQLite, attach PDFs, match PDFs to records, or supplement records with PDF content.

Use when the user wants to process new papers, patents, theses, documents, or proceedings from inbox queues into the knowledge base, run the ingest pipeline, or rebuild indexes.

Use when the user wants diagrams, flowcharts, architecture visuals, data relationships, timelines, concept maps, Mermaid, Graphviz, drawio, or polished paper figures generated from structured text or IR.

Use when the user wants Paper2Any-based paper-to-figure, PPT, poster, video, citation, rebuttal, DrawIO, mindmap, image, PDF-to-PPT, or KB workflows through the ScholarAIO Paper2Any MCP sidecar.

Use when the user wants to draft a literature review, survey a research area, summarize a field, organize workspace papers, identify gaps, or export review references.

Use when the user says a paper, review, report, or LaTeX deliverable is final and wants it archived under published/ or exposed through the static published-paper site.

Use when the user wants to ingest web URLs, online PDFs, rendered web pages, standards, manuals, or articles through qt-web-extractor into the normal document-ingest workflow.

Use when the user needs help choosing or organizing an academic-writing workflow by deliverable, stage, or format, including review articles, guided reading, paper sections, PPT or slides, posters, and technical reports.

Use when the user wants to browse arXiv preprints, search arXiv directly, fetch a PDF by arXiv ID or URL, or send a preprint into the ScholarAIO ingest pipeline.

Use when the user wants to check paper-library data quality, diagnose missing metadata, filename issues, DOI duplicates, title mismatches, or repairable metadata problems.

Use when the user wants to back up ScholarAIO data through configured rsync targets, inspect backup plans, or run a dry-run backup before syncing.

Use when working on bioinformatics workflows such as alignment, variant calling, phylogenetics, or protein-structure analysis, especially across BLAST, minimap2, samtools, bcftools, MAFFT, IQ-TREE, or ESMFold.

Use when the user wants to verify citations in AI-generated or human-written text against the local knowledge base and catch hallucinated, wrong, or missing references.

Use when the user asks about highly cited papers, citation rankings, or updating citation counts from external APIs.

Use when the user wants to create or inspect DOCX, PPTX, or XLSX files, generate Office deliverables, or verify layout and content with scholaraio document inspect.

Use when the user wants LLM-based metadata enrichment, table-of-contents extraction, L3 conclusion extraction, or abstract backfilling for library papers.

Use when the user wants to survey a journal or field, fetch papers from OpenAlex, cluster topics, build exploration embeddings, or search named explore libraries under data/libraries/explore.

Use when the user needs BibTeX, RIS, Markdown reference lists, filtered citation exports, custom citation styles, or a Markdown-to-DOCX export for sharing.

Use when the user asks about citation relationships, references, citing papers, shared references, bibliographic overlap, or graph-style paper connections.

Use when working on biomolecular molecular dynamics with GROMACS, including system setup, equilibration, production runs, trajectory analysis, or MM/PBSA-style post-processing.

Use when the user wants to analyze research behavior, search hot keywords, most-read papers, reading trends, active workspaces, or unread semantic neighbors.

Use when working on classical materials simulations with LAMMPS, including potential selection, shock or deformation setups, thermodynamic runs, or structure analysis for solids and nanomaterials.

Use when the user asks about LLM token usage, API call timing, runtime metrics, cost signals, or performance statistics.

Use when working on CFD cases with OpenFOAM, including solver selection, dictionary setup, mesh workflows, turbulence models, or flow and heat-transfer verification.

Use when the user wants guided reading, deep reading, or structured analysis of a single paper, starting from fuzzy keywords or a research question.

Use when the user wants help drafting or revising a research paper section, including Introduction, Related Work, Method, Results, Discussion, or Conclusion.

Use when the user has a patent publication number, patent URL, or patent-search result and wants the PDF fetched into the configured patent inbox.

Use when the user wants USPTO patent discovery, patent metadata lookup, application lookup, or downloadable patent candidates before ingest.

Use when the user needs an academic poster, conference poster, poster-style visual summary, section planning, figure-text balance, or poster packaging workflow.

Use when working on first-principles materials calculations with Quantum ESPRESSO, including SCF, band structures, DOS, phonons, electron-phonon coupling, Fermi surfaces, or charge density.

Use when the user wants to normalize paper directory names to Author-Year-Title format after metadata correction or audit cleanup.

Use when the user wants to identify research gaps, open questions, unexplored areas, cross-paper limitations, or future directions from workspace literature.

Use when the user receives peer review comments and wants a rebuttal, response letter, point-by-point reply, or evidence-backed revision response.

Use when serving scientific CLI tasks through ScholarAIO, especially when the agent should prefer scholaraio toolref, handle partial coverage safely, or avoid turning user work into documentation maintenance.

Use when adding or upgrading ScholarAIO support for a scientific computing tool, especially official docs ingestion, toolref integration, lightweight skill design, and end-to-end CLI verification.

Use when incrementally reviewing and repairing low-quality metadata after enrich, especially non-standard documents that need title, author, or year correction while skipping already reviewed records via .scrubbed.