USW
Systems & Synthetic BiologyMetabolic ModelingHardSeed

Design a heterologous pathway for a target metabolite

Use flux-balance analysis to design gene insertions/knockouts that maximize product yield.

Dr. Camille Dubois
Synthetic Biology Center
Computational design of microbial cell factories
Nature Catalysis · 2023
~5 h
registered 2025-07-11
FBApathwaymetabolic-engineering

End goal

Reach ≥ 80% of theoretical maximum product yield in silico.

Overview

The agent searches reaction databases for a route to the target, integrates it into a genome-scale model, and optimizes knockouts to push flux toward the product while preserving growth.

Tools allowed

1
COBRApy (FBA)·Terminal

Workflow

1-step protocol

Each step is verified against the scientist's targets. Open any simulation to test it live.

  1. 1

    Route & optimize

    Step 1 / 1

    Find a route and optimize flux toward the product.

    Protocol

    1. aSearch a heterologous route.
    2. bIntegrate into the model.
    3. cOptimize knockouts.

    Targets

    Product yield≥80% of max
    Growth retention≥30% WT
    Expected output

    A pathway + knockout design with predicted yield.

    Simulations · click to test