Metabolic Pathways Analysis: A Linear Algebraic Approach - Mathematical Concepts and Methods in Modern Biology - page 257

FIGURE 8.6
Graph for A −→ B + C .

FIGURE 8.7
Graph for system (8.19), external fluxes added.

Let's start by looking at the following abstract biochemical process:
⎧
⎨

A −→ B + C ,

B −→ D ,

(8.19)

C −→ E ,

⎩

D + E −→ F .

Suppose that A is an input to the system and F is an output. According to our directed
graph conventions, this system has the following representation as in Figure 8.7 .
To analyze this system with ExPA , we need to create an input file. An input file
for ExPA provides the program with a list of internal fluxes (labeled in the chapter as
v i ) and exchange fluxes (labeled in the chapter as b i ). A biochemical reaction can be
reversible or irreversible . All of the reactions in our abstract system are irreversible.
Based solely on our directed graph, our input file should look like Table 8.1 .