Biology Reference
In-Depth Information
FIGURE 1.8
DVD v1.0 main page screenshot.
as input and returns the wiring diagram and information about the state space of the
network including fixed points, number of components, cycles, and cycle lengths.
For systems with a relatively small number of variables, DVD can also compute and
display the entire space transition diagram. For larger networks, given any initial
state, DVD can compute and display the trajectory of this initial state. DVD is fairly
intuitive, well documented, and easy to use. In this chapter we will use DVD v1.0
available under the link with the same name from DVDs main page (Figure
1.8
). A
link to an online tutorial is available on the same page (see [
12
] for more details). Our
next example illustrates the use of DVD.
Example 1.4.
Assume we want to analyze the behavior of a Boolean network with
four nodes with the following set of transition functions:
x
1
(
t
+
1
)
=
f
x
1
(
x
1
(
t
),
x
2
(
t
),
x
3
(
t
),
x
4
(
t
))
=
x
2
(
t
)
x
2
(
+
)
=
f
x
2
(
x
1
(
),
x
2
(
),
x
3
(
),
x
4
(
))
=
x
3
(
)
∧
x
4
(
)
t
1
t
t
t
t
t
t
x
3
(
+
)
=
f
x
3
(
x
1
(
),
x
2
(
),
x
3
(
),
x
4
(
))
=
x
2
(
)
∧
x
4
(
)
t
1
t
t
t
t
t
t
x
4
(
t
+
1
)
=
f
x
4
(
x
1
(
t
),
x
2
(
t
),
x
3
(
t
),
x
4
(
t
))
=
x
1
(
t
)
∧
x
2
(
t
)
∧
x
3
(
t
).
In DVD, the number of nodes under “Network Description” should be set to four; the
number of states for each node should be two (since only the Boolean values 0 and
1 are allowed); the format for the input functions should be set to Boolean, and the
updating schedule should be set to synchronous (see Figure
1.8
).
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