Experimental data as time-dependent input in COPASI 

Implementing systems with forcing functions as exogenous input (COPASI .cps file).

Experimental data in lookup table, implemented as a time-dependent, piecewise defined function using events.

Lookup table with experimental time-course data:

time
[min]
input data
0.04339
150.14100
300.41646
450.51149
600.41065   
900.25279 
1200.14389
1800.07045
2400.04854

Species:
Reactions:
Global Quantities:

Create Rate Law for rate of appearance reaction as product of a kinetic parameter (ka) and a modifier (input data, between double quotes to form one single string from the two words):

create rate law

Rate of appearance reaction Ra, with input I as modifier:

Ra reaction

Model reactions:

reactions

Resulting differential equation model:


differential equation model

Create events to implement piecewise constant, time-dependent parameter. User-defined functions with logical operators.

first event

Repeat this for all datapoints in the lookup table. Overview of all 9 events:

all 9 events

Simulation window in COPASI:

simulation window COPASI

Simulation results:

data plot simulation result plot