neuroflow

Infinite improvement loop for any research artifact in any phase — a single managing agent makes one focused change per iteration, judges it against the previous best, keeps or reverts. Its memory is a per-loop wiki it reads before every move and writes after every move. The loop never stops until the human interrupts it. Inspired by Andrej Karpathy's autoresearch (MIT).

Phase guidance for /git — context-aware git shorthand rules, smart push/pull logic, commit message generation, branch management, and PR creation workflow.

This skill should be used whenever the user mentions BIDS, Brain Imaging Data Structure, BIDS conversion, BIDS validation, BIDS compliance, organizing neuroimaging data, dataset_description.json, participants.tsv, bids-validator, pybids, MNE-BIDS, or asks how to structure EEG/MEG/fMRI/iEEG/PET/DWI data for sharing or preprocessing. Also invoke when the user asks how to name scan files, what sidecar JSON fields are needed, how to set up derivatives/, or how to run fMRIPrep/MRIQC on their dataset. Invoke proactively during /data, /data-preprocess, and /data-analyze phases whenever the dataset structure is relevant to the task at hand.

Phase guidance for the neuroflow /data-analyze command. Loaded automatically when /data-analyze is invoked to orient agent behavior, relevant skills, and workflow hints for the data-analyze phase.

Phase guidance for the neuroflow /data-preprocess command. Loaded automatically when /data-preprocess is invoked to orient agent behavior, relevant skills, and workflow hints for the data-preprocess phase.

Phase guidance for the neuroflow /data command. Loaded automatically when /data is invoked to orient agent behavior, relevant skills, and workflow hints for the data intake phase.

Core rules and lifecycle for all neuroflow commands and agents. Read this whenever running any neuroflow command to understand the .neuroflow/ folder structure and the required behaviour at the start and end of every command.

Team-level knowledge layer for neuroflow. Connects a researcher's personal neuroflow project to a shared GitHub organisation repo for team identity, research directions, projects registry, knowledge base, meetings, tasks, and cross-project ideas. Never automatically copies personal project data — all sharing is explicit.

Phase guidance for the /meeting command. Covers meeting file structure, recurring templates, attendee resolution from profiles, Google Calendar MCP integration, agenda preparation with project context, and action-item-to-task conversion at all three levels (project, flowie, hive).

Knowledge base skill — Karpathy-style LLM-maintained wiki at three levels (personal/flowie, project, team/hive). Handles ingest, query, lint, schema, and project-tagging workflows. Invoked by /flowie --wiki-* (personal), /wiki (project), /hive --wiki-* (team).

Phase guidance for the neuroflow /flowie command. Covers how to read and use the flowie profile for personalization, write rules for ~/.neuroflow/flowie/, GitHub sync protocol, and profile-aware assistance across all phases.

Phase guidance for the neuroflow /notes command. Loaded automatically when /notes is invoked to orient agent behavior, relevant skills, and workflow hints for the notes phase.

Configure neuroflow integrations — Miro, Google Workspace, and custom LLM providers. Use when setting up credentials, checking integration status, or guiding a user through connecting external services. Also covers e-INFRA CZ connection for Czech academic researchers.

Worker-critic agentic loop protocol — orchestrator coordinates a worker agent and a critic agent across up to 3 revision cycles to produce a vetted output for any phase.

Phase guidance for the neuroflow /ideation command. Loaded automatically when /ideation is invoked to orient agent behavior, relevant skills, and workflow hints for the ideation phase.

Guide for developing and maintaining the neuroflow plugin. Use when adding skills, commands, agents, or hooks to neuroflow, bumping the version, or publishing updates to GitHub.

Remove AI writing signatures from prose. Makes text sound genuinely human-authored — varied rhythm, natural register, no AI tells. Use when drafting, editing, or reviewing any text that needs to read as if a person wrote it.

Phase guidance for /grant-proposal with deep funder knowledge, neuroscience-specific grant tactics, review criteria alignment, and workflow orchestration.

Phase guidance for the neuroflow /paper command. Loaded automatically when /paper is invoked to orient agent behavior, relevant skills, and workflow for the unified paper phase — covering manuscript drafting and rigorous internal peer review in a single write→critique loop.

Phase guidance for the neuroflow /poster command. LaTeX academic conference poster generation — template selection (A0/A1/A2, portrait/landscape, custom conference sizes), QR code integration, content extraction from project memory, and iterative poster-critic review loop.

Phase guidance for the neuroflow /review command. Loaded automatically when /review is invoked. Orients Claude for acting as a formal peer reviewer of a colleague's neuroscience paper.

Phase guidance for the neuroflow /write-report command. Loaded automatically when /write-report is invoked to orient agent behavior, relevant skills, and workflow hints for the write-report phase.

Run a rigorous pre-submission peer review of a neuroscience manuscript. Use this skill whenever the user asks to review, critique, or give feedback on a neuroscience paper, draft manuscript, or scientific write-up — whether they say "review my paper", "check my manuscript before submission", "act as a referee for my paper", "give me feedback on this neuroscience paper", or simply upload/paste a neuroscience manuscript and ask for comments. Also trigger when the user mentions fMRI, EEG, connectivity analysis, computational neuroscience, brain dynamics, or related topics in the context of evaluating written work. Covers all neuroscience subfields including systems, cognitive, computational, clinical, and complex-network approaches.

Phase guidance for the neuroflow /pipeline command. Loaded automatically when /pipeline is invoked to orient agent behavior for planning and executing multi-step research pipelines.

Phase guidance for the neuroflow /fails command. Orients agent approach for logging user dissatisfaction, categorising complaints accurately, and preparing GitHub issue reports.

Complete API for Google NotebookLM — full programmatic access including features not in the web UI. Create notebooks, add sources (URLs, YouTube, PDFs, audio, video, images), generate all artifact types (podcast, video, slide deck, infographic, report, quiz, flashcards, mind map), and download results in multiple formats. Activates on explicit /notebooklm or intent like "create a podcast about X", "turn this into an audio overview", "generate a quiz from my research", "make an infographic", or "create a slide deck".

Phase guidance for the neuroflow /experiment command. Loaded automatically when /experiment is invoked to orient agent behavior, relevant skills, and workflow hints for the experiment phase.

Phase guidance for the neuroflow /output command. Orients agent approach for outputting project memory or the whole project safely and with correct exclusions.

Lightweight search skill for the /search command. Instructs the agent to use flow.md files as a fast index, scope the search by tag (project or memory), and return a concise summary to the main agent.

Phase guidance for the neuroflow /slideshow command. Loaded automatically when /slideshow is invoked to orient agent behavior, slide structure decisions, format selection, and audience calibration for presentation generation.

Phase guidance for the neuroflow /tool-build command. Loaded automatically when /tool-build is invoked to orient agent behavior, relevant skills, and workflow hints for the tool-build phase.

Connect to Pupil Labs Neon eye-tracking glasses and collect real-time data streams (video, gaze, IMU, events). Use when working with Neon hardware via the Real-time API for live data visualization, data collection, or eye-tracking applications requiring device discovery, multi-threaded streaming, or hardware troubleshooting.

Create new skills, modify and improve existing skills, and measure skill performance. Use when users want to create a skill from scratch, edit, or optimize an existing skill, run evals to test a skill, benchmark skill performance with variance analysis, or optimize a skill's description for better triggering accuracy.

Phase guidance for the neuroflow /brain-build command. Loaded automatically when /brain-build is invoked to orient agent behavior, relevant skills, and workflow hints for assembling computational brain models.

Phase guidance for the neuroflow /brain-optimize command. Loaded automatically when /brain-optimize is invoked to orient agent behavior, relevant skills, and workflow hints for parameter search and model fitting.

Phase guidance for the neuroflow /brain-run command. Loaded automatically when /brain-run is invoked to orient agent behavior, relevant skills, and workflow hints for running brain model simulations.

Phase guidance for the neuroflow /quiz command. Loaded automatically when /quiz is invoked to orient behaviour, question quality, and mode-specific workflow for neuroscience quiz sessions.

Phase guidance for the neuroflow /tool-validate command. Loaded automatically when /tool-validate is invoked to orient agent behavior, relevant skills, and workflow hints for the tool-validate phase.

Phase guidance for the neuroflow /finance command. Loaded automatically when /finance is invoked to orient agent behavior, relevant skills, and workflow hints for grant document management and expense tracking.

Phase guidance for the neuroflow /preregistration command. Loaded automatically when /preregistration is invoked to orient agent behavior, relevant skills, and workflow hints for creating and managing pre-registration documents.