Accelerating the pace of engineering and science

Synthetic Biology and Metabolic Engineering with MATLAB and SimBiology

Sven Mesecke, MathWorks

From bulk chemicals and complex natural products to biologicals – the fields of Synthetic Biology, Metabolic Engineering and Bioprocess Development are increasingly combined for the engineering of biological systems.

Introduction of new genes and modification of existing genes have complex effects on the behavior of biological reaction networks. Mathematical modeling, simulation and optimization of these networks aid in the understanding and guiding of genetic modifications and support the rational design for maximal product yield. At later developmental stages, models assist in the design, scheduling, control and quality assurance of production processes.

This webinar will provide metabolic engineers and synthetic biologists with an introduction to cellular modeling and optimization with MATLAB and SimBiology using a real life example of engineering yeast cells for the overproduction of succinate. As a potential substitute for petrochemically produced polymer building blocks, biologically-produced succinate has a great potential of becoming one of the fundaments of a bioeconomy.

Target Group: Scientists and engineers from academia and industry using cells as (bio-)chemical plants.


  • import metabolic networks and other pathways from KEGG
  • use parallelized parameter sweeps to account for parameter uncertainties
  • use optimization to identify optimal perturbation/knock-out targets

Product Focus

  • SimBiology
  • Optimization Toolbox

Recorded: 10 Nov 2011