Complex systems and Biological physics seminar [before December 2013]

Simplification of complex metabolic networks by finding relevant pathways using optimization

Name: Simplification of complex metabolic networks by finding relevant pathways using optimization
Start: 2013-12-10T13:30:00+01:00
End: 2013-12-10T14:30:00+01:00
Location: No location set

by Erika Hagrot (KTH Biotechnology), Hildur Æsa Oddsdóttir (KTH Biotechnology)

Tuesday 10 Dec 2013, 13:30 → 14:30 Europe/Stockholm

122:026

Description

Elementary flux modes (EFMs) are pathways through a metabolic reaction network that connect external substrates to products. In EFMs-based metabolic flux analysis (MFA), experimentally determined external fluxes are used to estimate the flux of each EFM. Thereby the network description can be simplified by considering only the EFMs with nonzero flux. It is in general prohibitive to enumerate all EFMs for complex networks, since the number of EFMs increases rapidly with network complexity. We will present an optimization based method that dynamically generates a subset of EFMs and solves the EFMs-based MFA problem simultaneously. Furthermore we will present a case-study where the method was examined, using real data from a Chinese hamster ovary cell culture. The case-study showed that the EFMs-based MFA problem could be solved for a complex network at a low computational cost.