wshlavacek
commented
6 years ago It would probably look something like the code below, which is from Fig 8 in "Modeling for (physical) biologists: an introduction to the rule-based approach" (2015) Phys Biol.
begin model
A model of a genetic toggle switch
In this model, a transcriptional repressor, X, inhibits the synthesis
of a second repressor, Y, which inhibits the synthesis of X.
Repression is captured using the following function:
1/(1+([repressor]/K)^n).
Reference:
1. Gardner TS, Cantor CR, Collins JJ (2000) Nature 403: 339-342.
begin parameters
Note that parameter values are different from those chosen in Ref 1.
maximum rate of synthesis of repressor X
bx 50 # [=] molecules per cell per unit time
maximum rate of synthesis of repressor Y
by 50 # [=] molecules per cell per unit time
rate constant for clearance of X (through degradation and dilution)
ax 1 # [=] per unit time
rate constant for clearance of Y (through degradation and dilution)
ay 1 # [=] per unit time
parameters in the function characterizing Y's effect on synthesis of X
nyx 3 # [=] dimensionless Kyx 20 # [=] same units as Y()
parameters in the function characterizing X's effect on synthesis of Y
nxy 3 # [=] dimensionless Kxy 20 # [=] same units as X()
initial abundance of X
Xinit 0 # [=] copies per cell
initial abundance of Y
Yinit 0 # [=] copies per cell
end parameters
begin molecule types
Repressor 1
X()
Repressor 2
Y()
end molecule types
begin species X() Xinit Y() Yinit end species
begin observables Molecules X_tot X() Molecules Y_tot Y() end observables
begin reaction rules
synthesis of X according to a user-defined rate law
0 is a source.
0->X() bx/(1+(Y_tot/Kyx)^nyx)
clearance of X (through degradation and dilution)
0 is a sink.
X()->0 ax
synthesis of Y according to a user-defined rate law
0->Y() by/(1+(X_tot/Kxy)^nxy)
clearance of Y
Y()->0 ay
end reaction rules
end model
begin actions
generate_network({overwrite=>1})
Write ODEs for chemical kinetics of the generated network in a MATLAB M-file
writeMfile()
set initial system state close to the stable steady state where
expression of repressor X is off.
setConcentration("X()",0) setConcentration("Y()",50)
find steady states as a function of Kxy, which reflects the strength
of X's repression of Y.
Values of Kxy are scanned from the minimum specified value to the maximum.
Values are also scanned in the opposite direction.
If bistability exists, this procedure will find both steady states at each
tested value of the bifurcation parameter in the bistable region.
bifurcate({parameter=>"Kxy",par_min=>1.0,par_max=>1.0e2,n_scan_pts=>100,\ log_scale=>1,method=>"ode",t_start=>0,t_end=>1000,n_steps=>10,\ steady_state=>1})
end actions
On Fri, Feb 23, 2018 at 5:25 AM, Marco Antoniotti notifications@github.com wrote:
Hi
I would like to use the repressilator example in a course I am teaching, but I need a crash course on how it is rendered in BNGL.
Is there anybody who could help me?
I offer a pizza :) Cheers
Marco Antoniotti
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jrfaeder
lh64
Hi
I would like to use the repressilator example in a course I am teaching, but I need a crash course on how it is rendered in BNGL.
Is there anybody who could help me?
I offer a pizza :)
Cheers
Marco Antoniotti