A wide range of computational techniques aimed at identifying in silico metabolic engineering strategies for enhanced product synthesis have been presented in the research literature. These methods exploit the detailed pathway descriptions in genome-scale metabolic reconstructions to find gene knockouts and/or expression changes predicted to maximize synthesis of a target metabolite. While the Constraint-Based Reconstruction and Analysis (COBRA) toolbox contains functions that implement many metabolic engineering methods, users must write their own customized codes around these functions to develop useful workflows. Consequently, the power of in silico metabolic engineering has been limited to academic and industrial experts.
To bridge this knowledge gap, In Silico Fermentation is offering a training course focused on the use of genome-scale metabolic reconstructions for in silico cellular engineering. The training focuses on the identification of gene knockout strategies for metabolite overproduction while also covering more advanced methods which identify combinations of gene knockouts, overexpressions and underexpressions. Key concepts are demonstrated through computational exercises using Escherichia coli metabolic reconstructions of varying complexity. Each topic includes an interactive exercise where participants can implement the presented method on a metabolic model of their choice with assistance from the instructor as necessary. Participants complete the training with customized MATLAB codes and the hand-on experience necessary to incorporate in silico metabolic engineering in their research and development efforts..
The training is specifically designed for on-line delivery in time blocks defined by the participants to maximize work flexibility and information retention. The full course with interactive exercises can be covered in 24 on-line hours, while abbreviated versions presented with more traditional lectures can be completed in as little as 8 on-line hours. The course can be offered to 6-12 individual registrants or directly to employees from a single organization to allow a more customized training experience.
Main Topics
1. Implementing gene knockouts in metabolic reconstructions
2. Analyzing growth-production tradeoffs in gene knockout models
3. Computational design of gene knockout strains
4. Using the MATLAB Constraint-Based Reconstruction and Analysis (COBRA) toolbox
5. Utilizing the InSilicoKO app for gene knockout strain design
6. Computational identification of gene expression modifications
Course participants are expected to have some limited practical experience with the following topics:
1. Metabolic reconstructions and constraint-based analysis
2. Metabolic engineering
3. MATLAB or comparable high-level programming language
Please contact me by email if you would like to receive additional details about this training course, including cost and scheduling information.
