Commands

Run commands with /neuroflow:<command> in any project folder. Always start with /neuroflow:neuroflow.

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The research pipeline

neuroflow models a complete neuroscience research lifecycle. Commands pass context to each other through .neuroflow/ project memory, so each phase picks up where the last left off.

flowchart LR
    A["/ideation"] --> B["/experiment"]
    A --> C["/grant-proposal"]
    B --> D["/tool-build"]
    D --> E["/tool-validate"]
    E --> F["/data"]
    F --> G["/data-preprocess"]
    G --> H["/data-analyze"]
    H --> I["/paper"]
    I --> J["/review"]

Tip

You don't have to follow the pipeline in order. Jump to whichever phase you're in — neuroflow will read your project memory and orient itself.

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Entry points

Command	What it does
/neuroflow	Main entry point — scans your project, sets up .neuroflow/, or shows current status
/setup	Interactive wizard for PubMed and Miro credentials

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Research pipeline

Command	Phase	What it does
/ideation	ideation	Brainstorm, literature search, formalize a research question, write proposal
/preregistration	preregistration	Pre-register study design and analysis plan on OSF or AsPredicted; log deviations
/grant-proposal	grant-proposal	Full grant application — aims, significance, innovation, approach, budget
/finance	finance	Budget planning, expense tracking, financial reports, and grant compliance
/experiment	experiment	PsychoPy paradigm, recording setup, LSL/marker configuration
/tool-build	tool-build	Build lab tools — real-time systems, BCI, acquisition pipelines
/tool-validate	tool-validate	Testing pipeline for timing, markers, data output, edge cases
/data	data	Data inventory, BIDS validation, format conversion
/data-preprocess	data-preprocess	Filtering, ICA, epoching, artifact rejection, QC
/data-analyze	data-analyze	ERPs, time-frequency, connectivity, decoding, GLM
/paper	paper	Unified manuscript writing — draft section by section, write→critique loop
/review	review	Peer review a colleague's paper — structured referee report
/notes	notes	Live note-taking — capture rough input, reformat into a clean document
/write-report	write-report	Generate a structured report from .neuroflow/ for any phase or the whole project

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Brain simulation

Command	What it does
/brain-build	Assemble a computational brain model — neuron models, network topology, connectivity, simulation framework setup
/brain-optimize	Run a parameter search or fit the model to experimental data
/brain-run	Run the model as a simulation — configure run parameters, launch, and collect outputs

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Utility commands

Command	What it does
/git	Context-aware git utility — smart push/pull, commit message generation, branch management, and PR creation with shorthand aliases
/pipeline	Define and run a multi-step research pipeline — interactive by default (pauses for approval between steps), or use --executor for brutal mode
/output	Export project memory or the whole project — pack as a zip archive or copy to a folder for sharing, archiving, or handoff
/search	Lightweight scoped search — use memory: to search .neuroflow/ or project: to search the codebase
/interview	Interview preparation from either side — generate tailored questions, run practice Q&A, evaluate readiness
/phase	Show current phase and all phases worked on; optionally switch phase
/sentinel	Full audit of .neuroflow/ — drift detection, broken references, version sync
/quiz	Neuroscience quiz — flashcards, pub quiz, or rapid-fire throw questions
/fails	Log dissatisfaction — record plugin behavior, science quality, or UX issues; optionally opens a GitHub issue
/idk	Personal support companion — decompress, break down overwhelming tasks, or just chat

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How commands work

Every command follows the same lifecycle:

1. Read skills — Claude loads the phase-specific skill (e.g. neuroflow:phase-ideation) for domain guidance
2. Read project memory — Claude reads project_config.md and flow.md to orient itself
3. Do the work — Claude interacts with you to complete the phase task
4. Write outputs — Results go into the phase subfolder inside .neuroflow/
5. Update memory — flow.md and project_config.md are updated; a session entry is appended

This means every command is context-aware — it knows your research question, your modality, your tools, and what's been done before.