Metabolic Pathways Analysis: A Linear Algebraic Approach - Mathematical Concepts and Methods in Modern Biology - page 254

phylogenetics discussed in Chapter 10 of this volume, to explore the evolution of
metabolic pathways [ 17 , 18 ].
8.3 EXTREME PATHS AND MODEL IMPROVEMENTS
This final section was coauthored by Robert J. Kipka and Terrell L. Hodge.
In this section (which could be a stand-alone project), we'll use software to find
extreme paths. These are particular elements of the nullspace of a stoichiometric
matrix for which all nullspace elements are nonnegative linear combinations. This
section will allow us to explore some of our modeling assumptions in greater depth
and to do some simple analysis of the biochemistry of a red blood cell. The objectives
of this section are:
a. To reflect on the advantages and disadvantages of representing biochemical pro-
cesses using directed graphs.
b. To consider directed hypergraphs as a possible alternative and to interpret extreme
pathways using directed hypergraphs.
c. To develop some basic familiarity with the ExPA program for finding extreme
paths of complex biochemical systems.
The first thing we'll do is download ExPA and make sure it can run on your
computer.
8.3.1 Downloading and Installing expa.exe
The software we'll use for this section is available for free download at the following
Website:
http://gcrg.ucsd.edu/Downloads/ExtremePathwayAnalysis .
The program is meant to be run from a terminal window. If you're using a PC,
you can download an additional file from http://booksite.elsevier.com/
9780124157804 that allows you to run the program without having to deal with
the terminal window. If you're using a Mac, things are more complicated. At the time
of this writing, the program will not run at all on OSX 10.7 or later. If you're using
OSX 10.6 or older, the program will probably run but you will have to use a terminal
window. We encourage you to do so! Very little terminal use is required and the
benefits far outweigh the small amount of difficulty the terminal window represents.
8.3.1.1 InstructionsforaPC
To ins t a l l ExPA on your PC, follow the following steps in the order they're given.
1. Open a Web browser and go to http://gcrg.ucsd.edu/Downloads/
ExtremePathwayAnalysis .