ZimoLiao/scholaraio

backup

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

لغة النص الأصلي: الصينية

scientific-tool-onboarding

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

لغة النص الأصلي: الصينية

setup

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

لغة النص الأصلي: الصينية

academic-writing

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.

لغة النص الأصلي: لغات متعددة

document

Use when the user wants to create or inspect DOCX, PPTX, or XLSX files, generate a downloadable Office deliverable, or verify its structure and layout warnings with scholaraio document inspect.

لغة النص الأصلي: الصينية

draw

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.

لغة النص الأصلي: الصينية

paper-guided-reading

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

لغة النص الأصلي: الصينية

paper2any

Use when the user explicitly requests Paper2Any or a Paper2Any benchmark for paper-to-figure, PPT, poster, video, DrawIO, PDF-to-PPT, or related workflows through the isolated ScholarAIO sidecar.

لغة النص الأصلي: الصينية

webextract

Use when a URL or online PDF needs ingestion-ready rendered content, or when host-native URL reading failed because JavaScript/PDF rendering is required; only use it for those cases, not routine web discovery or reading.

لغة النص الأصلي: الصينية

ingest-link

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.

لغة النص الأصلي: الإنجليزية

nature-workflow

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,…

لغة النص الأصلي: الإنجليزية

patent-search

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

لغة النص الأصلي: الصينية

index

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

لغة النص الأصلي: الصينية

search

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.

لغة النص الأصلي: الصينية

import

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.

لغة النص الأصلي: الصينية

ingest

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.

لغة النص الأصلي: الصينية

literature-review

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.

لغة النص الأصلي: الصينية

publish

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.

لغة النص الأصلي: الإنجليزية

arxiv

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.

لغة النص الأصلي: الإنجليزية

audit

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

لغة النص الأصلي: الصينية

bioinformatics

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.

لغة النص الأصلي: الصينية

citation-check

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.

لغة النص الأصلي: الصينية

citations

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

لغة النص الأصلي: الصينية

enrich

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

لغة النص الأصلي: الصينية

explore

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.

لغة النص الأصلي: الصينية

export

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

لغة النص الأصلي: الصينية

graph

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

لغة النص الأصلي: الصينية

gromacs

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

لغة النص الأصلي: الصينية

insights

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

لغة النص الأصلي: الصينية

lammps

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.

لغة النص الأصلي: الصينية

metrics

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

لغة النص الأصلي: الإنجليزية

openfoam

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

لغة النص الأصلي: الصينية

paper-writing

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

لغة النص الأصلي: الصينية

patent-fetch

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.

لغة النص الأصلي: الصينية

poster

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

لغة النص الأصلي: الإنجليزية

quantum-espresso

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.

لغة النص الأصلي: الصينية

rename

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

لغة النص الأصلي: الصينية

research-gap

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

لغة النص الأصلي: الصينية

review-response

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

لغة النص الأصلي: الصينية

scientific-runtime

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.

لغة النص الأصلي: الإنجليزية