order of metabolites in stoichiometric matrix not consistent depending on where it is run

[janisshin]

when I call r.getFullStoichiometryMatrix(), the order of the metabolites changes depending on whether the method is called in a class or in a Jupyter notebook. From what I can tell, the order of the reactions remains constant.

Since I am passing in the stoichiometry matrix back and forth for matrix operations, the consistency of the order of the metabolites is crucial. Can you make the order consistent like the order of reactions? Thanks.

[hsauro]

That’s very odd. The only thing that can affect the order is the order you declare the species in the antimony model. You need to gives some examples that show that behavior.

[janisshin]

Also, when I call r.getFloatingSpeciesIds(), the order is different in a Jupyter notebook (first image) than when I call it in a class (second image).

In the second image, r.getIndependentFloatingSpeciesIds() is stored in variable a and r.getFloatingSpeciesIds() is stored in variable b.

[janisshin]

Okay, I think I got to the bottom of the issue.

import tellurium as te

# load the Teusink model
ant_file = 'data/interim/Antimony/BIOMD0000000064_e.ant'
r = te.loada(ant_file)
print(r.getFullStoichiometryMatrix())

ant_file = 'data/interim/Antimony/BIOMD0000000064_e.ant'
s  = te.loada(ant_file)
s.steadyState()
print(s.getFullStoichiometryMatrix())

For some reason, running s.steadyState changes the order of the floating species.

[hsauro]

Try setting the conservation flag to true first H

…

On Wed, Sep 6, 2023 at 11:50 AM Janis Shin ***@***.***> wrote: Okay, I think I got to the bottom of the issue. import tellurium as te # load the Teusink model ant_file = 'data/interim/Antimony/BIOMD0000000064_e.ant' r = te.loada(ant_file) print(r.getFullStoichiometryMatrix()) ant_file = 'data/interim/Antimony/BIOMD0000000064_e.ant' s = te.loada(ant_file) s.steadyState() print(s.getFullStoichiometryMatrix()) For some reason, running r.steadyState changes the order of the floating species. [image: image] <https://urldefense.com/v3/__https://user-images.githubusercontent.com/49432660/266110084-69b90e8e-203f-4ec0-9560-dc3d503e81a2.png__;!!K-Hz7m0Vt54!hD0DS3V2nY6jl1F-PJtBqjNwQxSDo_-58hayp68yg6U8CWOWsZdA0x3F2kMobHPHHodA-tKyalTHFQ4Uwi9r6TVgWR-pxA$> — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/sys-bio/roadrunner/issues/1143*issuecomment-1708915800__;Iw!!K-Hz7m0Vt54!hD0DS3V2nY6jl1F-PJtBqjNwQxSDo_-58hayp68yg6U8CWOWsZdA0x3F2kMobHPHHodA-tKyalTHFQ4Uwi9r6TXO-ElRbw$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AAIBSDQZDJHFOJKPPXNFKGTXZDAWZANCNFSM6AAAAAA4NXO26E__;!!K-Hz7m0Vt54!hD0DS3V2nY6jl1F-PJtBqjNwQxSDo_-58hayp68yg6U8CWOWsZdA0x3F2kMobHPHHodA-tKyalTHFQ4Uwi9r6TVcfd6a6g$> . You are receiving this because you commented.Message ID: ***@***.***>

[janisshin]

this generally works, but if I'm converting my antimony to sbml for running on Cobra, then Cobra uses the order of metabolites that is the same order as the one prior to running conservation on antimony. So, it would be nice if we could always just use one order instead of having the user be responsible for converting each time the model is loaded in both antimony and cobra.