Network Storage & Format
Contents
Representing the networks as graphs
2
Storage format for the networks
3
Organization of the network files
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
Network Storage & Format 1 of 4
Representing the networks as graphs
A graph contains vertices, which are the items, nodes, objects, etc., and edges, which define
the relationships between the vertices by connecting them. For reaction networks, the species
and reactions are represented as vertices and the edges represent how the species are
involved in the reactions. In a bipartite graph, there exist two distinct types of vertices where
edges can only connect vertices of different types. For reaction networks, reaction vertices can
only connect to species vertices but reactions cannot connect to other reactions and species
cannot connect to other species. In a directed graph, the edges indicate direction, usually with
an arrow, to indicate the flow, movement, conversion, etc. from one vertex to another. For a
reaction network, the edges that connect the vertices are directed to indicate the role of the
species in the reaction. Every edge is incident on one species vertex and one reaction vertex,
and all edges incident on one reaction vertex creates one reaction. The multigraph allows
multiple edges between a given pair of reaction and species, which can be used to represent
autocatalysis. The reaction networks are therefore represented as directed bipartite multigraphs,
as illustrated in Figure 1.
A) Species Vertex
1
B) Reaction Vertex
0
C) Uni-uni Reaction
1
D) Bi-bi Reaction
1
0
2
3
0
2
4
Figure 1. The parts of a network and how reactions are constructed.
Network Storage & Format 2 of 4
Storage format for the networks
Networks are represented as a list of pairs of vertices. Each pair represents a directed edge
between a reaction vertex and a species vertex. The first vertex in the pair is the source and the
second vertex is the target. For example, a uni-uni reaction (figure 1C) can be represented by its
edges: 1 → 0, 0 → 2, or more concisely as 1 0 0 2. A bi-bi reaction (figure 1D) could be
represented as 1 → 0, 2 → 0, 0 → 3, 0 → 4, or more concisely as 1 0 2 0 0 3 0 4. Using this method,
a network with 3 reactions and 5 species would have 3 reaction vertices, labeled 0 to 2, and 5
species vertices, labeled 3 to 7. If we had the network in Figure 2, it would be represented as 0 3
0 4 5 0 7 0 6 1 1 7 1 7 2 6 7 2 7 2. For all the networks stored in the repository, the number of
reactions and the number of species are added to the beginning of the string: <#reactions>
<#species> <pairs of edges>. For the network in Figure 2, it would be stored as: 3 5 0 3 0 4 5 0 7 0
6 1 1 7 1 7 2 6 7 2 7 2.
1
3
2
0
4
6
7
5
Figure 2. A reaction network with three reactions and five molecular species. The reactions in this
network are: 6 → 7 + 7, 7 + 7 → 6, and 5 + 7 → 3 + 4.
Network Storage & Format 3 of 4
Organization of the network files
All networks that have the same number of max in|out degree, species, and reactions are
stored in the same file. The file name indicates these values:
d_d<# max in|out degree>s<#species>r<#reactions>.txt
Each network is on one line in the file (i.e. each network is followed by a single line break).
Network Storage & Format 4 of 4