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Fig. 2. The enzyme-catalyzed process of glucose into glucose-6-phosphate is modeled using a simple Petri net. The left side
shows one abstract glucose molecule, one abstract enzyme hexokinase and energy (ATP). The right side shows the result of this
biochemical reaction*.
Fig. 3. This Petri net represents an abstract gene-controlled biochemical reaction. Fundamental processes like protein synthesis
and gene regulation can be modeled and integrated*.
are useful for the representation of qualitative reactions. Figure 2 shows a Petri net representation of a
simple enzyme-controlled reaction.
The disadvantage of this application is that neither complex metabolic processes nor quantitative
processes can be modeled. With the more complex Petri net language devised by Hofest adt [Hofestadt,
1994], it was shown that the Petri net concept can also model gene-controlled metabolic networks (Fig. 3)
and cell communication processes.
It was important to include the modeling of kinetic effects. Therefore the functional Petri net was
defined. The parameters of the Petri net language were extended [Hofest adt and Thelen, 1998], which
now allows the kinetic simulation of metabolic networks by placing specific functions to the arcs. Based
on the definition of the self modifying Petri net [Valk, 1978] a functional Petri net is a 5-tuple
FPN
=
(
P
,
T
,
F
,
V
F
,
m
0
) where (
P
,
T
,
F
) is a net and
V
F
is a mapping, which assigns each
f
from
F
a mapping
V
F
(
f
) and
V
F
(
f
) is an element of:
{
g
(
x
1
,
...
,
x
n
)
|
g
:
P
N
×
...
×
P
N
IN
,
n
∈
}
.
IN
*A colored version of the figure/chart is available at
In Silico Biol.
10
, 0003 <
http://www.bioinfo.de/isb/2010/10/0003/
>
, 1
February 2010.
