Graph Support Users’ Guide
Contents
Using the programs
2
File Formats
2
Running the programs
2
Graph2Jarnac
3
Graph2Matrix
4
For more information on this project: http://www.sys-bio.org/NetworkEnumeration
For information on our other projects: http://www.sys-bio.org
Anastasia Deckard
January, 2008
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Using the programs
This group of programs aids in working with the graph formats, including translations into
common network formats. Currently, we provide two programs for translating graphs into Jarnac
Script (graph2jarnac) and stoichiometry matrices (graph2matrix). These are console
applications. These programs use a common library, graphsupport.lib, for working with the
graphs.
File Formats
These programs will translate the graph format we are using in our network enumeration files (for
information please see the documentation for the network enumeration software at http://
www.sys-bio.org/NetworkEnumeration). The graph file can be one of the files downloaded from
our website or a graph file that you have made by collecting graphs together into a file. Graphs
with different #reactions and # species can be collected into a single file for processing. The
format of the file must be one graph per line in the format:
<#reactions> <#species> <pairs of edges>
For each graph in a graph file, the program will create one file with the name of the graph
(<#reactions> <#species> <pairs of edges>).
Running the programs
To run the program, it requires two arguments: the path to the graph file you wish to process and
the path to the directory where you would like the network files written:
<program> <graph file> <output directory>
For example, if you started the command line on a Windows machine and the program was
located at C:/graphsupport/graph2jarnac.exe, your graph file was located at C:/nets/
mynetworks.txt, and you wanted the files written to C:/jarnacfiles/, then you would enter this in
the command line:
C:/graphsupport/graph2jarnac.exe C:/nets/mynetworks.txt C:/jarnacfiles/
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Graph2Jarnac
The graph2jarnac program translates graphs in a file into separate Jarnac files. Jarnac is a
language for describing and manipulating cellular system models. The program for running
Jarnac files and also tools translating them into the Systems Biology Markup Language (SBML)
are available as part of the Systems Biology Workbench (SBW). SBW and associated information
can be found at: http://www.sys-bio.org/sbwWiki/sysbio/sbw. The Jarnac files have the
extension of “.jan”.
To run this program use:
graph2jarnac <graph file> <output directory>
For example, the following graph with three reactions and two species:
3 2 0 3 0 3 4 0 1 3 4 1 3 2 2 4
Would create this Jarnac file, named 3_2_0_3_0_3_4_0_1_3_4_1_3_2_2_4.jan:
//NETWORK SET: s 2 r 3
//NETWORK ID:
3_2_0_3_0_3_4_0_1_3_4_1_3_2_2_4
p = defn cell
R0: s1 -> s0 + s0;s1 * k0;
R1: s1 -> s0;s1 * k1;
R2: s0 -> s1;s0 * k2;
end;
p.s0 = 1;
p.s1 = 1;
p.k0 = 1;
p.k1 = 1;
p.k2 = 1;
The amount of the species and the rate constants are all set to 1, as the graphs do not carry any
information about these. Also note in the graph format the three reactions are numbered 0 to 2
and the species are numbered 3 to 4. However, in the Jarnac format the species are
renumbered starting at zero, so they are species 0 and 1 in the Jarnac file.
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Graph2Matrix
The graph2matrix program translates the graphs in a file into separate files each containing a
stoichiometry matrix representing a network. The matrix files have and extension of “.mat”.
To run this program use:
graph2matrix <graph file> <output directory>
For example, the following graph with three reactions and two species:
3 2 0 3 0 3 4 0 1 3 4 1 3 2 2 4
Would create this Jarnac file, named 3_2_0_3_0_3_4_0_1_3_4_1_3_2_2_4.mat:
//NETWORK SET:
//NETWORK ID:
2
1
-1
-1
-1
1
s 2 r 3
3_2_0_3_0_3_4_0_1_3_4_1_3_2_2_4
Graph Support 4 of 4