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Handbook
Handbook
00 — Frame
00 — Frame
Why this stack
Why interactivity
Single-author fragility
10 — BIDS
10 — BIDS
Strict raw root
Derivatives and manifest
BIDS beyond electrophysiology
20 — DataLad
20 — DataLad
Superdataset and subdatasets
Siblings and RIA
Code as subdataset
30 — Snakemake
30 — Snakemake
Rules and the DAG
Snakebids and wildcards
Config-driven pipelines
Three idioms
40 — Marimo
40 — Marimo
Reactive cells
Analysis notebooks
Handbook explorables
50 — Publication
50 — Publication
MkDocs for the site
Quarto for deliverables
Two surfaces, one cross-link protocol
60 — projio
60 — projio
The stack-aware layer
notio (project memory)
pipeio (pipelines as data)
biblio + indexio
figio + manuscript
codio (code as catalog)
70 — Agentic
70 — Agentic
Claude Code and MCP
Permissions and bounded context
Skills
Captures, tasks, queues
80 — Orchestration
80 — Orchestration
Worklog overview
Goals and critical path
Cross-project dispatch
90 — Future directions
90 — Future directions
Agent hierarchies
Live agent-agent communication
Honest gaps
References
Outline (spec)
Tutorials
Tutorials
Quickstart
Ecosystem Overview
Project Setup Workflow
Note-Driven Workflow
Semantic Search Pipeline
Agent-Driven Ingestion
Shared Code Library
Agent Orchestration
Grand Routine
Research Orchestration (Questio)
Site & Docs Workflow
Marimo Reactive Notebooks
Presentio Deck Iteration
How-To Guides
How-To Guides
Initialize A Workspace
Configure The MCP Server
Manage DataLad Siblings
Build The Documentation Site
Set Up A Dev Environment
Build A Quarto Report
Presentio Cross-Project Imports
Explanation
Explanation
Ecosystem
Delegation Model (Engineering vs. Science)
Ecosystem Architecture
Workspace Architecture
Package Integration
Search Before Creation
Agent Safety & Permissions
Research Orchestration (Questio)
Presentio (Decks as Artifacts)
Reference
Reference
CLI
Workspace Layout
Configuration
MCP Tools
Skills
Specs
Specs
pipeio
pipeio
Overview
Registry
Flow Config
Path Resolution
Notebook Lifecycle
Scaffolding
Contracts
CLI
MCP Tools
Deliverables
Research Orchestration (Questio)
Research Orchestration (Questio)
Research Orchestration Layer — Design Spec
Loop Mechanisms
Scenario Book
Scenario Book
Scenario Book — Agentic Research Workflows
TTL Removal
Anomaly Investigation
Reproduce Paper
Method Evaluation
Cross-Flow Debug
Manuscript Drafting
Unexpected Finding
Research Sprint
Skills
Skills
Questio Investigate
Questio Iterate
Questio Record
Deliverables
Deliverables
Reports
Presentations
Posters
Log
Log
Commit
Daily
Idea
Issue
Meeting
Personal
Result
Task
Weekly
Weekly
Table of contents
Contents
Table of contents
Contents
Weekly
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Contents
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