Biology Reference
In-Depth Information
Logical operators:
&
stands for the
AND
operator (conjunction),
|
stands for the
OR
operator (disjunction), and
˜
stands for the
NOT
operator (negation).
Constraint Definition
Possible constraints are classified as vertex-dependent (
include, exclude, position
),
path-
dependent
(
length, score
),
and
result-dependent
constraints
(
shortest, longest, lowest,
highest
). The names of vertices are not case sensitive.
Vertex-dependent constraints:
Include
(
i
)
ensures the occurrence of a given vertex in the path. This means in biological sense that
the path has to include a special enzyme or metabolite.
Exclude
(
e
)
ensures the absence of a given vertex in the path. Special enzymes or metabolites are
excluded explicitly, e.g., for knockout simulations.
Position
(
p
)
ensures the occurrence of a given vertex at a specified position in the path.
This
constraint is much stronger than the include constraint.
Syntax:
i
{
x
}
finds paths containing vertex
x
, e.g.,
i
{
AT P
}
.
i
{
x, y
}
is equivalent to (
i
{
x
}
&i
{
y
}
). It finds paths containing vertices
x
and
y
, e.g.,
i
{
eSuc,
Suc
}
.
Analogously, the same syntax is valid for
exclude
(
e
)
.
p
{
x, n
}
finds paths containing vertex
x
at position n, e.g.,
p
{
AT P, 4
}
.
p
{
x, end
}
finds paths containing vertex
x
at the last position, e.g.,
p
{
eSuc, end
}
.
{
x, end-n
}
finds paths containing vertex
x
at the last the position minus n, e.g.,
p
{
Suc, end-2
}
.
p
Path-dependent constraints:
These constraints refer to the whole path length. Length (k) compares the length of the computed path
with the previously defined length k using the relations greater than, smaller than, and equals to. Score
(s) compares the score s, defined as the sum of the edge weights along the path, with the previously
defined score s using the relations greater than, smaller than, and equals to.
Syntax:
l
{
>, n
}
as well as
lmin
(
n
) give paths with equal or more vertices than n, e.g.,
lmin
{
4
}
.
l
{
<, n
}
as well as
lmax
(
n
) give paths with equal or less vertices than n, e.g.,
lmax
{
15
}
.
l
{
=, n
}
as well as
l
{
n
}
give paths with exactly n vertices, e.g.
l
{
10
}
.
Analogously, the same syntax is valid for
score
(
s
)
.
These vertex- and path-dependent constraints can be combined by the given logical operators (AND,
OR, and NOT). Because of the possibility of combining constraints by these operators and of using
brackets, each other logical standard operator, e.g., NAND, NOR, XOR, and others can be described.
Result-dependent constraints:
These constraints are not evaluated on one path, but on the set of all computed paths. This type of
constraints can not be connected by logical operators. Each defined constraint string can contain only