Preliminary bare-bones page for BERIL

Author: nlharris

project/BERIL/index.md

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+---
+layout: project
+title: BERIL
+active: true
+funding: DOE BER
+homepage: 
+github: 
+logo: 
+---
+
+## BERIL: Integrated AI Infrastructure for Genome-to-Phenotype Research Using the BER Data Lakehouse
+
+BERIL is a new (late 2025) $4M project funded by the Department of Energy’s department of Biological and Environmental Research (BER).
+The BER Data Lakehouse seeks to provide consistently labeled, harmonized datasets designed for AI-driven reasoning and inference across multiple heterogeneous data sources.
+The **BER** **I**ntegrative **L**ayer will develop an extensible, self‑updating AI ecosystem 
+that leverages the BER Data Lakehouse to orchestrate specialized reasoning agents and accelerate genome‑to‑phenotype discovery.
+
+BERIL’s unified agentic AI infrastructure includes a Central Orchestration Agent (Generalist Agent)
+working collaboratively with multiple Specialized Agents.
+The Generalist Agent coordinates overall activities and user interaction and facilitates literature searches, tool execution and Data Lakehouse queries.
+It also manages "reasoner traces," collecting detailed records of reasoning processes and engaging in rationale-driven refinement loops.
+This dual-layer feedback approach combines curiosity-driven interactions (reasoner traces) and formal benchmarking.
+The integrated agent coordination framework will employ a hybrid approach, combining curiosity-driven exploration and
+structured modular extensions via the Model Context Protocol (MCP).
+
+As a pilot demonstration of BERIL, we will select genes, pathways,
+and microbial strain targets that support DOE BER biomanufacturing and bioproduct development objectives.