Correction in ODE output

[anugnair]

The ODE output generated by the tellerium getODEFromX() methods is missing the volume normalization term, which is quite confusing. I have a simple model:

species drugExtraVenous, drugCentral, drugPeripheral;

drugExtraVenous in extraVenous;
drugCentral in central;
drugPeripheral in peripheral;

drugExtraVenous -> drugCentral; ka_Central*drugExtraVenous*extraVenous;                     # absorption
drugExtraVenous -> ; kcl_extraVenous*drugExtraVenous*extraVenous;                           # non-bioavailable fraction
drugCentral => drugPeripheral; Q12*drugCentral - Q12*drugPeripheral;    # distribution phase
drugCentral -> ; clearance*drugCentral;                                                  # elimination phase

central = 1                          # liter
peripheral = 1                       # liter
extraVenous = 1                        # liter
ka = 1                                 # 1/hour
F = 1
ka_Central = ka * F                       # 1/hour
kcl_extraVenous = ka * (1-F)              # 1/hour
clearance = 1                         # liter/hour
Q12 = 1                                 # liter/hour

All the species are in the concentration units, and of course the reaction rates are in amount/time unit. I get meaningful simulation output where it seems that rate equation evaluations are normalized by the compartment volume to get the left-hand side species concentration. However, when I look at the equations generated by te.getODEsFromModel(), the volume normalization terms are not present on the right-hand side of the ODEs. I get the following ODEs:

v_J0 = ka_Central*drugExtraVenous*extraVenous
v_J1 = kcl_extraVenous*drugExtraVenous*extraVenous
v_J2 = Q12*drugCentral-Q12*drugPeripheral
v_J3 = clearance*drugCentral

ddrugExtraVenous/dt = (-v_J0 - v_J1)
ddrugCentral/dt = (v_J0 - v_J2 - v_J3)
ddrugPeripheral/dt = v_J2

Shouldn't the correct ODEs be the following?

ddrugExtraVenous/dt = (-v_J0 - v_J1) / extraVenous
ddrugCentral/dt = (v_J0 - v_J2 - v_J3) / central
ddrugPeripheral/dt = v_J2 / peripheral

Best regards,
Anu

[hsauro]

That is quite possible, but shouldn't be difficult to fix however. Herbert Sauro

…

On Wed, Feb 12, 2025 at 2:09 PM anugnair ***@***.***> wrote: The ODE output generated by the tellerium getODEFromX() methods is missing the volume normalization term, which is quite confusing. I have a simple model: species drugExtraVenous, drugCentral, drugPeripheral; drugExtraVenous in extraVenous; drugCentral in central; drugPeripheral in peripheral; drugExtraVenous -> drugCentral; ka_Central*drugExtraVenous*extraVenous; # absorption drugExtraVenous -> ; kcl_extraVenous*drugExtraVenous*extraVenous; # non-bioavailable fraction drugCentral => drugPeripheral; Q12*drugCentral - Q12*drugPeripheral; # distribution phase drugCentral -> ; clearance*drugCentral; # elimination phase central = 1 # liter peripheral = 1 # liter extraVenous = 1 # liter ka = 1 # 1/hour F = 1 ka_Central = ka * F # 1/hour kcl_extraVenous = ka * (1-F) # 1/hour clearance = 1 # liter/hour Q12 = 1 # liter/hour All the species are in the concentration units, and of course the reaction rates are in amount/time unit. I get meaningful simulation output where it seems that rate equation evaluations are normalized by the compartment volume to get the left-hand side species concentration. However, when I look at the equations generated by te.getODEsFromModel(), the volume normalization terms are not present on the right-hand side of the ODEs. I get the following ODEs: v_J0 = ka_Central*drugExtraVenous*extraVenous v_J1 = kcl_extraVenous*drugExtraVenous*extraVenous v_J2 = Q12*drugCentral-Q12*drugPeripheral v_J3 = clearance*drugCentral ddrugExtraVenous/dt = (-v_J0 - v_J1) ddrugCentral/dt = (v_J0 - v_J2 - v_J3) ddrugPeripheral/dt = v_J2 Shouldn't the correct ODEs be the following? ddrugExtraVenous/dt = (-v_J0 - v_J1) / extraVenous ddrugCentral/dt = (v_J0 - v_J2 - v_J3) / central ddrugPeripheral/dt = v_J2 / peripheral Best regards, Anu — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/sys-bio/roadrunner/issues/1256__;!!K-Hz7m0Vt54!hw56THfaaiY6_c1JGRbOIQDZhtqOzHqFFFBPFAqKCKCAGlfD7i-faVDVQzfAcv_vljkSUiaVPpEzgc7TNQXId0SfSoYZ6g$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AAIBSDRM4BM7REESLJVVCDT2PPBAXAVCNFSM6AAAAABXAWOX36VHI2DSMVQWIX3LMV43ASLTON2WKOZSHA2DSNBVGU3DAMA__;!!K-Hz7m0Vt54!hw56THfaaiY6_c1JGRbOIQDZhtqOzHqFFFBPFAqKCKCAGlfD7i-faVDVQzfAcv_vljkSUiaVPpEzgc7TNQXId0TmggJajQ$> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Herbert Sauro, Professor Director: NIH Center for model reproducibility University of Washington, Bioengineering 206-685-2119, www.sys-bio.org, http://reproduciblebiomodels.org/ Mobile: 206-880-8093 ***@***.*** Books: http://books.analogmachine.org/