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Lesson 31
10 min

Brenner Bot: Research

Coordinate multi-agent AI research with scientific methodology

New to ACFS?

Complete the setup wizard first to get the most from these lessons.

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Goal

Coordinate multi-agent AI research sessions with structured scientific methodology.

What Is Brenner Bot?

Brenner Bot is a research orchestration platform inspired by Nobel laureate Sydney Brenner's scientific methodology. It coordinates multi-agent AI research sessions with systematic problem formulation and rigorous constraint-based reasoning.

The system combines a curated corpus of 236 transcript sections with multi-model AI syntheses from Claude, GPT, and Gemini to enable collaborative scientific research conversations.

Primary Corpus

236 sections with §n citations

Multi-Model

Claude, GPT, Gemini syntheses

Hypothesis Slates

Always includes third alternative

Quote Bank

Searchable verbatim primitives

Scientific Methodology

Brenner Bot emphasizes rigorous scientific reasoning with these principles.

Problem Formulation

Clear statement of what you're trying to understand

Discriminative Design

Experiments that distinguish hypotheses

Third Alternative

Always consider "both hypotheses are wrong"

Constraint Reasoning

What data rules out, not just suggests

Quick Start

Get started with these essential commands.

Check installation
Run diagnostics
Search transcripts
Start research session
Pro Tip
Research sessions coordinate via Agent Mail. Make sure Agent Mail is running first.

Corpus Search

Search the primary source corpus for relevant passages.

Corpus Commands
# Search the transcript corpus
brenner corpus search "experimental design"
# List available sections
brenner corpus list
# Build excerpts from specific sections
brenner excerpt build --sections 42,43,44
# Export with citations
brenner excerpt build --sections 42-50 --format markdown
Note
Citations use stable §n format (e.g., §42) for reliable referencing.

Research Sessions

Launch multi-agent research workflows.

Start new session
Resume existing session
List active sessions

Sessions produce structured artifacts:

Hypothesis Slates — Multiple competing explanations
Discriminative Tests — Experiments that distinguish hypotheses
Assumption Ledgers — Explicit premises with verification
Adversarial Critiques — Challenges to the framing itself

Tool Integration

Brenner Bot integrates with other flywheel tools.

Brenner + Agent Mail

Research sessions use Agent Mail for durable threads between agents. Each agent has an inbox/outbox with acknowledgment tracking.

Brenner + NTM

NTM spawns parallel agent sessions for research. Use NTM to manage the tmux layout while Brenner coordinates the research flow.

Brenner + CASS

Research session history is indexed by CASS. Search past sessions to build on previous research findings.

Web Interface

The web app at brennerbot.org provides additional features.

Corpus Browsing — Full-text search with section navigation
Excerpt Composition — Build cited passages from selections
Session Visualization — View research session structure
Note
The CLI and web app complement each other—use CLI for automation and web for browsing.

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