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productivity-tools
329

cass

Coding Agent Session Search - unified CLI/TUI to index and search local coding agent history from Claude Code, Codex, Gemini, Cursor, Aider, ChatGPT, Pi-Agent, Factory, and more. Purpose-built for AI agent consumption with robot mode.

Dicklesworthstone
Dicklesworthstone
tools
open
design
328

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
ZimoLiao
content-media
open
machine-learning
328

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
ZimoLiao
data-ai
open
knowledge-base
328

napkin

Read, create, search, and manage notes in Obsidian vaults using the napkin CLI. Works directly on markdown files and canvas files — no Obsidian app required. Use when the user asks to interact with their Obsidian vault, manage notes, search vault content, work with tasks, tags, properties, daily notes, templates, bases, bookmarks, aliases, or canvas files from the command line.

Michaelliv
Michaelliv
documentation
open
knowledge-base
328

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.

ZimoLiao
ZimoLiao
documentation
open
knowledge-base
328

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
ZimoLiao
documentation
open
knowledge-base
328

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
ZimoLiao
documentation
open
technical-docs
328

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.

ZimoLiao
ZimoLiao
documentation
open
academic
328

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
ZimoLiao
research
open
academic
328

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.

ZimoLiao
ZimoLiao
research
open
academic
328

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
ZimoLiao
research
open
academic
328

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.

ZimoLiao
ZimoLiao
research
open
academic
328

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
ZimoLiao
research
open
academic
328

literature-review

Write a literature review based on papers in a workspace. Covers topic organization, narrative structure, gap identification, and BibTeX export. Use when the user wants to draft a literature review, survey a research area, or summarize the state of the art.

ZimoLiao
ZimoLiao
research
open
academic
328

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
ZimoLiao
research
open
academic
328

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
ZimoLiao
research
open
academic
328

insights

Analyze research behavior data — search hot keywords, most-read papers, reading trends, and semantic neighbors you haven't read yet. Use when the user wants to understand their reading habits, discover overlooked papers, or review recent research activity.

ZimoLiao
ZimoLiao
research
open
academic
328

research-gap

Identify research gaps and open questions from the literature in a workspace. Combines topic clustering, citation analysis, and cross-paper comparison. Use when the user wants to find unexplored areas, formulate research questions, or assess where the field is heading.

ZimoLiao
ZimoLiao
research
open
bioinformatics
328

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
ZimoLiao
research
open
computational-chemistry
328

lammps

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

ZimoLiao
ZimoLiao
research
open
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