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neuroflow0.2.31 · docs

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phase-ideation

The ideation phase is the entry point of a research project — sharpening a vague idea into a testable research question and mapping the existing literature rigorously.

Approach

  • Identify which entry point applies (brainstorm, literature explore, formalize, proposal, literature review) before doing anything else
  • Resist generating a full proposal before the research question is clear — sequence matters
  • Perform all literature searches inline by following skills/phase-ideation/references/search-protocol.md — do NOT spawn sub-agents
  • Save .md metadata stubs for all results and ask the user which papers to download
  • Download open-access copies only — never Sci-Hub; when no open copy exists, the person gets the paper through their institutional library access
  • After the user selects papers (or skips), use the literature-review agent to run the full 12-protocol analysis
  • The literature-review agent works from PDFs or .md stubs — full download is not required
  • Keep outputs hypothesis-driven and concise; avoid scope creep at this stage
  • If project_config.md already has a research question, confirm whether to refine or restart

Relevant agents

  • literature-review — runs 12 sequential analytical protocols on downloaded papers; checks each with a critic pass defined in the agent itself (rubric, mechanical checks first, up to 3 rounds, verdicts in the neuroflow:worker-critic format), saves each as a resumable checkpoint, and compiles the review to .neuroflow/ideation/literature-review-[date].md. The critic pass is a self-check by the same agent; /ideation can add an independent check by running the critic brief in a separate general-purpose agent.

Note: Literature searches are performed inline by the main agent following the search protocol — the scholar agent is NOT spawned as a sub-agent. Use the standalone scholar agent only for ad-hoc searches outside the /ideation workflow.

Relevant skills

  • neuroflow:neuroflow-core — read first; defines the command lifecycle and .neuroflow/ write rules
  • neuroflow:pupil-labs-neon-realtime — if the project involves Pupil Labs Neon eye-tracking hardware, use this skill for real-time data collection and device connection during ideation/piloting

Zotero integration (optional)

If a Zotero MCP server is connected (any mcp__*zotero* tools available), the literature workflow becomes library-first: search the user's Zotero library before external sources, mark already-owned papers 📚 in results (excluded from download offers), and pass the user's existing Zotero notes/annotations to the literature review in its brief. If no Zotero MCP is present, /ideation asks once whether to set one up (answer stored as zotero: in ~/.neuroflow/user.yaml — a personal preference, not a project fact; setup guidance lives in /setup). Never require Zotero — the plain stub-based flow is always the fallback.

Writing to Zotero is opt-in, never a default: adding items, collections, notes, tags or attachments happens only after the person confirms that specific write in the same turn.

Workflow hints

  • The research question produced here anchors every downstream phase — write it precisely
  • Save the final research question to .neuroflow/ideation/research-question.md
  • Update the research question in the markdown body of project_config.md if it is defined or changed (it is not a frontmatter key)
  • Downloaded papers live in .neuroflow/ideation/papers/ — this folder is the input for the literature-review agent
  • Standing queries live in .neuroflow/ideation/watch.md; recommend free PubMed / bioRxiv alerts for them, and add watch hits to papers/ only for the papers the person picks
  • The compiled literature review (literature-review-[date].md) feeds directly into the paper phase; reference it there
  • The search protocol reads skills/phase-ideation/references/journal-defaults.md to match the query to one of eight neuroscience areas and surface high-impact journals. If the user has custom journal preferences, they can create .neuroflow/journal-preferences.md from the template at skills/phase-ideation/references/user-journal-preferences.md.

Slash command

/neuroflow:ideation — runs this workflow as a slash command.