Brenner Bot: Research

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.

Research Session Cockpit|BR-0847

brenner-session

Corpus Query Fan-out2 sources

query

Transcription Studies§42-4814 hits

Protein Modification§49-559 hits

Hypothesis ConfidencePhase 1

H1: Transcriptionalleading

50%

H2: Post-translationalleading

50%

H3: Combinatorialleading

50%

Confidence trajectory

Knowledge Graph1 concepts

Transcription

t=0

Phase 1 of 6: Hypothesis Formulation17%

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