51

4.2

Useful Tools for Metabolic Modelling

­

4.1

4.2

4.2

2006

The YANA programs, which are programmed in Java and can therefore be used flex­

ibly on any computer, can be used to calculate not only the different flux possibilities for

metabolism, but also how strong the flux is in a particular situation, especially through a

single enzyme. The programs can analyze larger and larger networks faster and faster; a

genome-wide network is described in the 2011 paper (Schwarz et al. 2005, 2007; Cecil

et al. 2011).

CellNetAnalyzer (CNA) is a MATLAB toolbox. Via a graphical user interface, various

computer methods and algorithms are offered for the analysis of the structure of metabolic

networks as well as for the analysis of signaling networks and regulatory networks.

Metabolic networks are modeled using a stoichiometric matrix and boundary condi­

tions. Thus, CNA uses very similar principles of flux balancing as Metatool does with

elementary mode analysis. Their calculation is also offered as well as “minimal cut sets”

(how do I safely cut a metabolic pathway?). The different algorithms are also offered for

the construction of strains as well as for metabolic engineering (e.g. optimal yields in

biotechnology).

Table 4.1  Applications of metabolic modelling. (Dandekar et al. 2014)

Metabolic fluxes (“modes”) that occur only in

bacteria but not in humans

Antibiotics

Yield (final product) for given starting

product(s)

Biotechnology

Growth equation

Calculation of growth in plants, bacteria,

pathogens

Metabolic overview

Characterization of microbes and organisms

(Often from genome sequence)

Characterization of the adaptation potential,

identification of organisms

Calculation of robustness

Prediction of essential genes

4.2  Useful Tools for Metabolic Modelling