Compartments and ODEs

[bjornhald]

Hi,
Thanks for a really nice and flexible environment for sys-bio modelling & simulations.

I want to report a small "bug" that caused some headache re compartments. I'm unsure whether it relates to tellurium or roadrunner. Nevertheless, if I write up the same reactions for a standard 2-compartment PK model and load in models with without declaration of species in compartments, I get the same return when I ask for return of ODEs, but I also get different simulations!

s_pk = """
species Aabs = 0.0;          # drug SC
species Ac = 0.0;              # drug central
species Ap = 0.0;              # drug peripheral

compartment Vc = 1.34
compartment Vp = 0.35
compartment SC = 1

const ka = 1.23
const Q = 0.15     # L/h
const Cl = 0.62
const F = 1.0

Aabs -> Ac;  ka * Aabs                 # [nmol/h] absorption 
Ac -> Ap    ;   Q * (Ac - Ap)          # [nmol/h] 
Ac ->          ;   Cl * Ac          
"""

pk_comp = """
species Ac in Vc;
species Ap in Vp; 
species Aabs in SC; 
"""

dose = 5
r = te.loada(s_pk + pk_comp)
r.Aabs += r.F * dose  # SC dosis
y = r.simulate(0, 15, 151)         

r2 = te.loada(s_pk )
r2.Aabs += r2.F * dose  # SC dosis
y2 = r2.simulate(0, 15, 151)       

If I then ask for the ODEs

>>> te.getODEsFromModel(r))
>>> te.getODEsFromModel(r2))

both yields

v_J0 = ka*Aabs*SC
v_J1 = k12*Ac*Vc-k21*Ap*Vp
v_J2 = Ke*Ac*Vc

dAabs/dt = -v_J0
dAc/dt = v_J0 - v_J1 - v_J2
dAp/dt = v_J1

A plot of the two simulations, however, shows the difference. This is troubling. I can deduce that declaration of species in compartments makes tellurium divide the ODE of the relevant species with the volume of the compartment. But I cannot find info in the documentation.

Is there a way of handling dosing without having to write up reactions as amount/time?

Thanks in advance