Biology Reference
In-Depth Information
133
FIGURE 7.7
Screenshot of the SynBioSS DS including the reaction network and corresponding species underlying the proTeOn and proTeOff models.
3.
In the new window, click on
'
Add
'
to add a reaction,
'
Modify
'
to modify an existing reac-
tion, and
to delete an existing reaction. For the purposes of this study, the 32
biochemical reactions that describe the behavior of proTeOn and proTeOff were added
to build the representative reaction network. These reactions are shown in
Figure 7.7
in
the
'
Delete
'
column, and account for the process of transcription, translation, pro-
tein folding, degradation, and transport. To provide the reaction type (e.g. first order, sec-
ond order, Michaelis-Menten, etc.) for each reaction, click on
'
Reaction List
'
In this window,
you are also asked to define the reaction parameter(s) and reactant(s)/product(s), along
with their corresponding stoichiometric coefficients.
4.
Click on the boxes to the left of the species in the
'
Rate Law.
'
column (
Fig. 7.7
) to choose the
species you would like to save. Next, click on the boxes to the right of the species in the
'
'
Save
'
column to choose the species whose amount is halved during cell
division. Finally, provide the initial number of molecules for each species in the
Split on Cell Division
'
'
Initial
In
the proTeOn and proTeOff model all the above conditions were set in compliance with
the experimental work.
5.
The next step is to provide the simulation parameters. Click on
Amount
'
column. After providing all the conditions of the system, click on
'
OK.
'
'
Specify Simulation
Parameters
'
to open a new window. Here, click on
'
Number of Simulation Trajectories to
'
Generate
to provide the number of trials to consider. One hundred thousand trials have
typically been used such that the simulation results can be compared with the experi-
mental phenotype of 100 000 cells. Next click on
to define the sim-
ulation time. Seventy-two thousand has been a typical simulation time used to compare
'
End Time (seconds)
'
