FBA gives incorrect objective_value 0 for bigg models iMM1415 & iRC1080

[matthiaskoenig]

When comparing the results of simple FBA simulations of cobrapy with SBSCL the following two BiGG models give different results:

objective_value_cobrapy 	mid 	objective_value_sbscl 	identical
1.3634279056507832 	iMM1415 	0.0 	False
6.156851475936173 	iRC1080 	0.0 	False

[hemilpanchiwala]

@matthiaskoenig, These models now provide correct results in SBSCL. I have updated the changes in PR #54. So, should I link this issue to the PR so that it can be closed once PR gets merged?

Commits Link: c40ef21
9b92496

[hemilpanchiwala]

OPTIMAL LP SOLUTION FOUND
iMM1415.xml
Objective value: 1.3634279056663554

OPTIMAL LP SOLUTION FOUND
iRC1080.xml
Objective value: 6.156851475933738

[matthiaskoenig]

Yes, link the issue.

…

On Fri, Aug 7, 2020 at 6:48 PM Hemil Panchiwala ***@***.***> wrote: OPTIMAL LP SOLUTION FOUND iMM1415.xml Objective value: 1.3634279056663554 OPTIMAL LP SOLUTION FOUND iRC1080.xml Objective value: 6.156851475933738 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAG33OUW2L7FES7CD2BW4HDR7QV7JANCNFSM4FANYDVA> .

-- Matthias König, PhD. Junior Group Leader LiSyM - Systems Medicine of the Liver Humboldt Universität zu Berlin, Institute of Biology, Institute for Theoretical Biology https://livermetabolism.com konigmatt@googlemail.com https://twitter.com/konigmatt https://github.com/matthiaskoenig Tel: +49 30 2093 98435

[draeger]

OPTIMAL LP SOLUTION FOUND
iMM1415.xml
Objective value: 1.3634279056663554

OPTIMAL LP SOLUTION FOUND
iRC1080.xml
Objective value: 6.156851475933738

@hemilpanchiwala: It would be helpful to also state which software found which value and how large the divergence was. Which solver was used?

[hemilpanchiwala]

@draeger,

OPTIMAL LP SOLUTION FOUND
iMM1415.xml
Objective value: 1.3634279056663554

OPTIMAL LP SOLUTION FOUND
iRC1080.xml
Objective value: 6.156851475933738

These are the results provided by SBSCL.

While the results by cobrapy are

iMM1415.xml -> 1.363427906
iRC1080.xml -> 6.156851476

Deviations (sbscl_results - cobrapy_results):

iMM1415.xml -> -3.3364467e-10
iRC1080.xml -> -6.6261663e-11

[hemilpanchiwala]

I used the FluxBalanceAnalysis class to solve the model.

[draeger]

The divergence is only only the order of or even . This is already getting close to machine precision for some circumstances.