Biology Reference
In-Depth Information
one result-dependent constraint. Using these constraints optimal paths can be calculated. If there are
several optimal paths, all optimal paths will be provided.
Shortest
or
longest
gives the paths of
shortest
or
longest
length, respectively.
Lowest
or
highest
gives the paths with
lowest
or
highest
score, respectively.
Syntax:
shortest
finds shortest paths, e.g.,
i
{
AT P
}
|e
{
UTP
}
, shortest.
longest
finds longest paths, e.g.,
i
{
AT P
}
&e
{
UTP
}
, longest.
{
}
{
}
, lowest. highest finds paths with
lowest
finds paths with lowest score, e.g.,
i
AT P
|e
UTP
highest score, e.g.,
i
{
AT P
}
&e
{
UTP
}
, highest.
User-defined constraints:
The user has the possibility to define own constraints and save them in a separate file. They can also
be defined as standard constraints, but must be named.
In the current implementation there exist the
following pre-defined constraints.
Syntax:
nopi, e
{
Pi
}
finds paths without phosphates as vertices.
nopp, e
}
finds paths without diphosphates as vertices.
no
pp, nopi & nopp
finds paths without phosphates and diphosphates.
dijkstra, lowest
finds the path with the lowest score.
{
PP
Implementation
The software is implemented in Java version 1.4.2.
Thus, the program runs under Windows and
Linux/Unix.
RESULTS AND DISCUSSION
To demonstrate the functionality of the program we consider the Petri model of the sucrose-to-starch
breakdown in the potato tuber. The Petri net model is not very large, but, because of the many reversible
reactions and the graph density, complicated enough to show the usefulness of constraint definitions
to search for alternative paths. For a more detailed description and explanation of the modelling and
analysis approach see Koch
et al.,
2004.
The net is depicted in Fig. 2.
Abbreviations for enzymes,
metabolites, and reaction types are compiled in Table 1.
In the following we give examples for path searches. For this purpose, we have to give the start and
end vertex, followed by the constraint string.
Search without Constraints
eSuc-> starch "":
The search for all possible paths from eSuc to starch without constraints yields
171 paths.
