5.4 Methodology

The two methods used in this chapter are the flux estimating method Flux Balance Analysis (see Section 4.5.2) and the community detection method Markov Stability (see Section 2.3.1).

A very brief summary of both methodologies is shown in this section.

Flux Balance Analysis (FBA) (Orth, Thiele, and Palsson 2010; Rabinowitz and Vastag 2012) is a widely-adopted approach to analyse metabolism and cellular growth.

FBA calculates the reaction fluxes that optimise growth in specific biological contexts.

The main hypothesis behind FBA is that cells adapt their metabolism to maximise growth in different biological conditions.

The conditions are encoded as constraints on the fluxes of certain reactions; for example, exchange reactions that import nutrients and other necessary compounds from the exterior.

On the other hand, the communities in each network were extracted using the Markov Stability (MS) community detection framework (Delvenne, Yaliraki, and Barahona 2010; Delvenne et al. 2013).

This framework uses diffusion processes on the network to find groups of nodes (i.e., communities) that retain flows for longer than one would expect on a comparable random network; in addition, MS incorporates directed flows seamlessly into the analysis (Beguerisse-Díaz et al. 2014; Lambiotte, Delvenne, and Barahona 2014).