Edward Vitkin, Ph.D. Thesis Seminar
Efficient and sustainable conversion of biomass into valuable products is a major challenge for bioengineering.
The composition of the feedstock biomass and the ability of microorganisms to efficiently ferment it are two most
critical factors influencing the process efficiency. Intelligent design that addresses both these factors can greatly
benefit from organism metabolic models and from using them in simulations and in computer-assisted optimization of the
In this talk we will cover several aspects of such simulations. We will discuss the construction and improvement of single
organism metabolic models as well as present high-scale simulations to optimize multi-organism fermentation processes.
Even in the two-organism fermentation system, many tested scenarios, such as reaction knockout analysis,
may require solutions of millions of optimization tasks. We will present BioLEGO, a framework to support these heavy calculations,
which is deployed as a Microsoft Azure Cloud service, leveraging the associated parallel computing capacities.