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Agent skills
autoresearch

Topic: autoresearch

101 skills in this topic.

gromacs Use when working on biomolecular molecular dynamics with GROMACS, especially system setup, equilibration, production runs, trajectory analysis, or MM/PBSA-style post-processing.
ZimoLiao/scholaraio 332
graph Query citation graphs — view a paper's references, find which papers cite it, and analyze shared references between multiple papers. Use when the user asks about citation relationships, reference overlap, or bibliographic connections.
ZimoLiao/scholaraio 332
export Export papers from the knowledge base to standard citation formats (BibTeX, RIS, Markdown reference list) or export any Markdown content as a Word DOCX file. Supports exporting all papers, specific papers, or filtered by year/journal. Use when the user needs citation files, wants to import into Zotero/Endnote/Mendeley, needs a reference list for writing, or wants to share a document as Word.
ZimoLiao/scholaraio 332
explore Explore literature by fetching papers from OpenAlex with multi-dimensional filters (ISSN, concept, author, institution, keyword, etc.), building local embeddings, running BERTopic clustering, and multi-mode search (semantic/keyword/unified). Data is isolated in data/explore/<name>/. Use when the user wants to survey a journal, explore a research field, analyze an author's output, or do landscape analysis.
ZimoLiao/scholaraio 332
draw Generate diagrams and vector graphics. Supports Mermaid (flowcharts, sequence diagrams, ER diagrams, Gantt charts, mind maps) via mermaid-py, and custom vector graphics (shapes, text, gradients, layers) via cli-anything-inkscape. Outputs PNG/SVG/PDF to workspace/. Use when the user wants to visualize workflows, architecture, data relationships, research timelines, concept maps, or create polished figures for papers.
ZimoLiao/scholaraio 332
document Generate and inspect Office documents (DOCX, PPTX, XLSX). Generate by writing Python scripts that call python-docx, python-pptx, and openpyxl APIs directly. Inspect with `scholaraio document inspect` to verify layout, content, and catch issues (overflow, missing elements). Use when the user wants to create Word reports, PowerPoint presentations, Excel data sheets, or inspect any Office document.
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citations View top-cited papers ranking and refetch citation counts from APIs. Use when the user asks about highly cited papers, citation rankings, or wants to update citation data.
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citation-check Verify citations in AI-generated or human-written text against the local knowledge base. Catches hallucinated references, wrong metadata, and missing papers. Use when the user wants to check if citations are real and accurate.
ZimoLiao/scholaraio 332
bioinformatics Use when working on bioinformatics toolchains such as alignment, variant calling, phylogenetics, or protein-structure analysis, especially when the agent must route across BLAST, minimap2, samtools, bcftools, MAFFT, IQ-TREE, or ESMFold.
ZimoLiao/scholaraio 332
audit Audit paper data quality in the knowledge base. Checks for missing fields, filename issues, DOI duplicates, title mismatches, and more. Supports LLM-based deep diagnosis for title mismatches and automated repair. Use when the user wants to check data quality, find problems, or fix metadata issues.
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metrics View LLM token usage, API call timing, and runtime metrics. Use when the user asks about token consumption, API costs, or performance statistics.
ZimoLiao/scholaraio 332
openfoam Use when working on CFD cases with OpenFOAM, especially solver selection, dictionary setup, mesh workflow decisions, turbulence-model choices, and verification of fluid-flow or heat-transfer simulations.
ZimoLiao/scholaraio 332
paper-writing Assist with writing sections of a research paper (Introduction, Related Work, Method, Results, Discussion, Conclusion). Leverages workspace papers for citations and evidence. Use when the user wants help drafting or revising specific paper sections.
ZimoLiao/scholaraio 332
quantum-espresso Use when working on first-principles materials calculations with Quantum ESPRESSO, especially SCF, band structures, DOS, phonons, electron-phonon coupling, Fermi surfaces, or charge-density analysis.
ZimoLiao/scholaraio 332
rename Rename paper directories to standardized Author-Year-Title format based on JSON metadata. Use when the user wants to normalize filenames after metadata corrections.
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review-response Draft point-by-point responses to peer review comments. Locates supporting evidence from workspace papers and the original manuscript. Use when the user receives reviewer feedback and needs to write a rebuttal or revision response letter.
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scientific-runtime Use when serving scientific CLI tasks through ScholarAIO, especially when the agent should prefer scholaraio toolref, handle partial coverage safely, and avoid turning user work into documentation maintenance.
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scientific-tool-onboarding Use when adding or upgrading ScholarAIO support for a new scientific computing tool, especially when the work needs official docs ingestion, toolref integration, lightweight skill design, and end-to-end CLI verification
ZimoLiao/scholaraio 332
search Search academic papers in the local ScholarAIO knowledge base. Supports unified search (keyword + semantic fusion), keyword-only (FTS5), semantic-only (FAISS), author search, and federated search across main library, explore databases, and arXiv. Use when the user wants to find papers, look up literature, search by author, explore research topics, or search across multiple sources. For citation rankings and citation count updates, see the /citations skill.
ZimoLiao/scholaraio 332
setup Initialize and diagnose the ScholarAIO environment. Run interactive setup wizard (bilingual EN/ZH) to install dependencies, create config files, and configure API keys. Run status check to see what's installed and what's missing. Use when the user wants to set up, install, configure, or troubleshoot ScholarAIO.
ZimoLiao/scholaraio 332
show View paper content at different detail levels. L1 (metadata), L2 (abstract), L3 (conclusion), L4 (full text). Use when the user wants to read a paper, see its abstract, conclusion, or full content.
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topics Explore topic distribution in the paper library using BERTopic clustering. Build/rebuild topic models, view topic overview, list papers in a topic, merge similar topics, and generate HTML visualizations. Use when the user asks about research themes, topic distribution, or wants to discover cross-domain connections.
ZimoLiao/scholaraio 332
workspace Manage workspace paper subsets — create workspaces, add/remove papers, search within a workspace, and export BibTeX. Workspaces are thin layers that reference papers in the main library by UUID. Use when the user wants to organize papers into groups for writing, review, or focused analysis.
ZimoLiao/scholaraio 332
writing-polish Polish academic writing — remove AI-generated patterns, improve clarity, and match a target style. Supports both English and Chinese. Use when the user wants to refine prose, remove AI artifacts, or adapt writing to a specific journal style.
ZimoLiao/scholaraio 332