Metabolic Pathways Analysis: A Linear Algebraic Approach - Mathematical Concepts and Methods in Modern Biology - page 256

4. To use expa without the command prompt, all input has to be placed in this
“source.txt” file . When you double-click on “ run-expa.bat ,” the program
reads what's written in “source.txt” and writes its output to “paths.txt.”

8.3.1.2 InstructionsforaMac
The instructions for getting ExPA to run on a Mac are not as detailed as those for a PC.
This is because the programmay not even run on a Mac. At the time of this writing the
programwill not work on OSX10.7 and may not work on OSX10.6 without additional
effort. To install ExPA on a Mac, take the following steps:

1. Open a Web browser and go to http://gcrg.ucsd.edu/Downloads/
ExtremePathwayAnalysis .
2. Download “A new Mac ExPA program” to your desktop.
3. Open up your “Applications” folder and create a new folder called “expa.”
4. Copy the contents of the folder created by the download to the “expa” folder you
created in “Applications.”
5. Open a terminal window and type in “ cd /Applications/expa ”. Press
enter. This will change your working directory.
6. Type in “ ls ” and press enter. This command lists the contents of the directory
you're working in. Check that “macexpa.out” is in the list of files. If it's not, check
that you copied the contents of the downloaded folder (not the whole folder) to
the “expa” folder in “Applications.”
7. Once you've found “macexpa.out” using the terminal, type in “ chmod u + x
macexpa.out ”. This only needs to be done once. The program is now ready
to be used.
8. To test the program, type in “ ./macexpa.out./rbc.expa ”. The program
should create a file called “ paths.txt ”. This is how the program is run. Simply
navigate to the /Applications/expa directory and type in “ . /macexpa.
out ” followed by the name of your input file. The program only needs to be run
from the terminal window. The easiest way to edit input files or read output files
is with a text editor.

8.3.2 Analyzing a Modeling Decision: Directed Graphs
In representing biochemical reactions as directed graphs, we've chosen to represent
metabolites as vertices and place edges between vertices whenever the metabolites
are biochemically linked. For example, A −→ B + C appears in a directed graph as

in Figure 8.6 .
Of course, there's nothing that forces us to make this choice; this is a modeling
decision and comes with both strengths and weaknesses. In this section we'll explore
this decision in a little bit greater depth and consider an alternative representation. At
the end, we'll use our new understanding to analyze red blood cell metabolism using
ExPA .