Amsterdam Science Park Study Group

Genome sequencing and annotation have paved the way for the development of genome-scale constraint-based metabolic models (GEM) for various organisms¹. These GEMs computationally describe gene-protein-reaction associations across the entire metabolic network of an organism, allowing for the prediction of metabolic fluxes in a range of systems-level metabolic studies. This workshop will introduce computational modeling of genome-scale metabolic reaction networks through a scalable framework known as constraint-based modeling. Constraint-based modeling is a powerful modeling framework that allows to model reaction fluxes in genome-scale metabolic network models, with uses in fundamental and applied questions relevant to biotechnology, microbiology, etc^2,3. In this workshop, you will be introduced to:

• Content, structure and reconstruction of microbial genome-scale metabolic models
• The underlying mathematical foundations of constraint-based modeling
• Open source COBRA software, with a focus on the Python package COBRApy
• Two important methods of GEM manipulations: Flux balance analysis (FBA) and dynamic FBA

The workshop is structured into lectures and practical sessions so that theory can be illustrated with biologically motivated computational examples.  The program of the workshop for Thursday July 11^th:

• 13:00 – 13:45 Lecture Fundamentals of GEMs and an introduction to the COBRApy toolbox
• 13:45 – 14:30 Hands-on exercises with GEM model and basic COBRApy functions
• 14:30 – 14:45 Break
• 14:45 – 15:30 Lecture Introduction of microbial growth simulation
• 15:30 – 16:30 Hands-on exercises of FBA and dFBA

We anticipate 10-15 attendees. Register here: https://docs.google.com/forms/d/e/1FAIpQLSdt9ZxyK60pfwvZbBbYa7uAe-eKvnd15y6qkkuhLHkl9BNrVg/viewform?usp=sf_link

Note: Participants need to bring their own laptop with Python installed, need basic Python skills and will receive instructions about installing COBRApy before the workshop (otherwise they need to collaborate with participants who do have this).

1. Gu, C., Kim, G. B., Kim, W. J., Kim, H. U. & Lee, S. Y. Current status and applications of genome-scale metabolic models. Genome Biol 20, 121 (2019).
2. Heirendt, L. et al. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nat Protoc 14, 639–702 (2019).
3. Ebrahim, A., Lerman, J. A., Palsson, B. O. & Hyduke, D. R. COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Syst Biol 7, 74 (2013).