BrainPilot: Automating Brain Discovery with Agentic Research
BrainPilot is an open-source, human-supervised agent system for brain science that uses specialized agents, knowledge, skills, and tools to support research work. Researchers use it to review literature, plan studies, perform analyses, write reports, and check scientific claims. Its catalogue entries are skills and an MCP integration that extend or operate the BrainPilot research workflow.
Skill Claude CodeCodex
You MUST use this before any creative work - creating features, building components, adding functionality, or modifying behavior. Explores user intent, requirements and design before implementation.
Skill Claude CodeCodex
Use when facing 2+ independent tasks that can be worked on without shared state or sequential dependencies.
Skill Claude CodeCodex
Use when you have a written implementation plan to execute in a separate session with review checkpoints.
Skill Claude CodeCodex
Use when implementation is complete, all tests pass, and you need to decide how to integrate the work.
Skill Claude CodeCodex
Use when receiving code review feedback, before implementing suggestions, especially if feedback seems unclear or technically questionable - requires technical rigor and verification, not performative agreement or blind implementation.
Skill Claude CodeCodex
Use when completing tasks, implementing major features, or before merging to verify work meets requirements.
Skill Claude CodeCodex
Use when executing implementation plans with independent tasks in the current session.
Skill Claude CodeCodex
Use when encountering any bug, test failure, or unexpected behavior, before proposing fixes.
Skill Claude CodeCodex
Use when implementing any feature or bugfix, before writing implementation code.
Skill Claude CodeCodex
Use when starting feature work that needs isolation from current workspace or before executing implementation plans - ensures an isolated workspace exists via native tools or git worktree fallback.
Skill Claude CodeCodex
Use when starting any conversation - establishes how to find and use skills, requiring skill invocation before ANY response including clarifying questions.
Skill Claude CodeCodex
Use when about to claim work is complete, fixed, or passing, before committing or creating PRs - requires running verification commands and confirming output before making any success claims; evidence before assertions always.
Skill Claude CodeCodex
Use when you have a spec or requirements for a multi-step task, before touching code.
Skill Claude CodeCodex
Use when creating new skills, editing existing skills, or verifying skills work before deployment.
Skill Codex
Audit scientific implementation, exported-model equivalence, dependency completeness, manifests, packaging, and isolated inference. Use when claims depend on code, trained artifacts, evaluators, or deployable entry points.
Skill Codex
Audit scientific data semantics, sample and label alignment, leakage, group splits, preprocessing boundaries, and train-to-inference transforms. Use for any result based on datasets, feature matrices, tensors, repeated observations, or learned preprocessing.
Skill Codex
Audit numeric, artifact, log, citation, and cross-report claims against inspectable evidence. Use for reports, syntheses, benchmark claims, external citations, or conflicting Expert outputs.
Skill Codex
Coordinate iterative evidence and reliability reviews between BrainPilot's Principal Investigator and Auditor. Use when PI needs to audit its own draft, an Expert result, or a multi-agent synthesis; when Auditor receives such a review task; or when a previous audit requires correction and incremental re-review.
Skill Codex
Audit whether method discovery, comparison, representative real-data validation, collapse diagnostics, pruning, and selection evidence support claims of suitability or superiority. Use for research-method selection, empirical evaluation, benchmarking, modelling, prediction, or other conclusions that depend on choosing…
Skill Codex
Curate BrainPilot Trace Events into human-readable research Episodes, appropriately granular nodes, and direct dependson relationships. Use when a report contains multiple settings, results, analyses, visualizations, findings, or conclusions; when Episode placement is unclear; or when deciding whether new evidence…
Skill Codex
Create or update the canonical Markdown inventory of task-relevant research data. Engineer must invoke this skill before creating or updating any data inventory, data contract, or dataset-coverage summary that downstream agents will use.
Skill Claude CodeCodex
Research a bounded factual, documentation, API, or literature question from authoritative sources and save a self-contained Markdown report with claim-level citations. Use for reading-heavy evidence gathering, not experiment execution or data analysis.
Skill Claude CodeCodex
One-command skill contribution — generate a SKILL.md from your domain expertise and submit to GitHub Issues for maintainer review.
Skill Claude CodeCodex
Step-by-step guidance for contributing a new skill to the NeuroAIHub/awesomecognitiveandneuroscienceskills repository via GitHub Pull Request, including SKILL.md format requirements, quality rules, and PR checklist.
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: