Research Hub

research-hub

research-hub turns Zotero, Obsidian, and NotebookLM into an AI-operable research workspace. It works best with any two of the three tools, and unlocks the full loop when all three are connected.

Prerequisite check (do this first)

This skill drives the research-hub Python CLI. Before running any command from this skill, verify the CLI is installed:

research-hub doctor

If that command is not found (vs. emitting a health report), the user installed only the Claude Code marketplace plugin and is missing the Python CLI. Stop and tell them:

This skill needs the research-hub CLI. Please run:

pip install research-hub-pipeline
research-hub setup --persona researcher   # or analyst | humanities | internal

Then re-run your request. If you only need to compare papers, sharpen a research question, or build a project / paper memory file (no automated search, no NotebookLM upload), the marketplace install alone is enough — you don't need this skill for those.

Do not invent or simulate research-hub output if the CLI is missing.

Default language policy: answer the user in their language. Generate durable research notes, metadata, and citations in English unless the user explicitly asks for another language.

Pick The Right Entry Point

Setup Commands

pip install research-hub-pipeline[playwright,secrets]
research-hub setup
research-hub doctor

For local files without Zotero:

pip install research-hub-pipeline[import,secrets]
research-hub setup --persona analyst
research-hub import-folder ./papers --cluster my-local-review

Core Workflows

Preview

research-hub dashboard --sample

Research Topic

research-hub plan "TOPIC"
research-hub auto "TOPIC" --no-nlm
research-hub serve --dashboard

Use --no-nlm for first-run smoke tests or when NotebookLM browser automation is not configured.

Discover (search + AI fit-check)

Two-phase interactive flow when you want a human / AI in the loop on which papers actually belong in a cluster. Replaces the auto one-shot ingest when topic boundaries are fuzzy.

research-hub discover new --cluster project-topic --query "agent-based modeling flood adaptation"
# → emits search results + a fit-check scoring prompt; stashes state

# Run the fit-check prompt through your AI of choice, paste the scores back
research-hub discover continue --cluster project-topic --scores scores.json
# → applies scores, emits papers_input.json for ingest

research-hub fit-check {emit|apply|audit|drift} exposes the underlying gates separately when you want to re-score an existing cluster or audit drift over time. discover variants emits a query-variation prompt to widen recall before fit-check narrows it.

Local Source Folder

research-hub import-folder ./sources --cluster project-topic
research-hub serve --dashboard
research-hub crystal emit --cluster project-topic

NotebookLM

research-hub notebooklm login
research-hub notebooklm bundle --cluster project-topic
research-hub notebooklm upload --cluster project-topic
research-hub notebooklm generate --cluster project-topic --type brief
research-hub notebooklm download --cluster project-topic

Synthesize cluster pages

Generate or refresh per-cluster synthesis pages in the Obsidian vault (uses cluster memory + paper summaries to produce a navigable overview note).

research-hub synthesize --cluster project-topic
research-hub synthesize --cluster project-topic --graph-colors  # also paint the graph view

Run synthesize after paper-summarize has filled the per-paper notes; the synthesis page reads from those.

Cluster memory

Maintain a structured memory registry per cluster — durable notes the AI can reload across sessions without re-reading every paper.

research-hub memory list --cluster project-topic
research-hub memory read --cluster project-topic
research-hub memory emit --cluster project-topic   # AI extraction prompt
research-hub memory apply --cluster project-topic --payload memory.json

Use memory emit/apply to refresh the registry after a major round of new papers; use read from another session to reload context cheaply.

Maintenance

research-hub doctor --autofix
research-hub tidy
research-hub clusters rebind --emit
research-hub cleanup --all

MCP Integration

For MCP hosts:

{ "mcpServers": { "research-hub": { "command": "research-hub", "args": ["serve"] } } }

Install host-specific files:

research-hub install --platform claude-code
research-hub install --platform cursor
research-hub install --platform codex
research-hub install --platform gemini

Guardrails

• Always run research-hub doctor when setup state is uncertain.
• Do not invent DOIs, citations, or paper metadata; use search/enrich/verify commands.
• Do not delete clusters without reviewing cascade impact.
• Treat the vault as user-owned local data; avoid overwriting notes unless asked.
• Prefer import-folder for non-academic or internal documents.
• Prefer Zotero-backed workflows for DOI/arXiv-heavy academic literature.