scenario for a bug in pareto optimality

[hariszaf]

Hi there,

I am trying to figure out the Pareto optimality script of yours. I was wondering if there is any chance that in line 74 rxn2 should be replaced by rxn1. If I am mistaken then probably I still have not understood well how this approach works, so apologies in advance and if you could share anything to enlighten me it would be much appreciated.

Thanks a lot for your time and help!

I hereby confirm that I have:

• [x] Tried to solve the issue on my own
• [x] Retried to run my code with the latest version of The COBRA Toolbox
• [x] Checked that a similar issue has not already been opened

[rmtfleming]

what script specifically?

On Fri, 9 Dec 2022 at 12:02, Haris Zafeiropoulos @.***> wrote:

Hi there,

I am trying to figure out the Pareto optimality script of yours. I was wondering if there is any chance that in line 74 https://github.com/opencobra/cobratoolbox/blob/master/src/analysis/multiSpecies/microbiomeModelingToolbox/pairwiseInteractionModeling/computeParetoOptimality.m#L74 rxn2 should be replaced by rxn1. If I am mistaken then probably I still have not understood well how this approach works, so apologies in advance and if you could share anything to enlighten me it would be much appreciated.

Thanks a lot for your time and help!

I hereby confirm that I have:

• [ x ] Tried to solve the issue on my own
• [ x ] Retried to run my code with the latest version of The COBRA Toolbox
• [ x ] Checked that a similar issue has not already been opened

— Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/2093, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAQMEOT6BK4KP74G3PETK33WMMNUBANCNFSM6AAAAAASZIQAC4 . You are receiving this because you are subscribed to this thread.Message ID: @.***>

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Associate Professor, School of Medicine, National University of Ireland, Galway. & Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming

Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 852 109 806 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

[hariszaf]

In the computeParetoOptimality.m script https://github.com/opencobra/cobratoolbox/blob/master/src/analysis/multiSpecies/microbiomeModelingToolbox/pairwiseInteractionModeling/computeParetoOptimality.m#L74

[rmtfleming]

Hi Haris, yes, it looks like it should be model = changeObjective(model, rxn1); Please submit a PR with the fix. Regards, Ronan

On Fri, 9 Dec 2022 at 18:49, Haris Zafeiropoulos @.***> wrote:

In the computeParetoOptimality.m script

https://github.com/opencobra/cobratoolbox/blob/master/src/analysis/multiSpecies/microbiomeModelingToolbox/pairwiseInteractionModeling/computeParetoOptimality.m#L74

— Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/2093#issuecomment-1344649543, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAQMEOXDNRMZU3FO5ICLBELWMN5MFANCNFSM6AAAAAASZIQAC4 . You are receiving this because you commented.Message ID: @.***>

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Associate Professor, School of Medicine, National University of Ireland, Galway. & Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming

Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 852 109 806 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)