FindExcRxn returns non-Exc reactions

[kamoors]

I am currently manipulating a model to add a new compartment, so the structure looks like this:

[c] <-> [e] (new <->) [NewComp] (new <->) []

1) modified original EX reactions to be met[e] <-> met[NewComp] (instead of met[e] <-> []) 2) added a new EX reaction met[NewComp] <-> []

The problem is that for some when I add these reactions, SOME of the [e] <-> [NewComp] reactions appear in the output of FindExcRxns, despite them having [-1;1] stoichiometry. I double checked this both using the stoichiometry output of the FindMetsFromRxns function, and by inspecting model.S for those functions.

Does anyone have an idea what could be causing this and how to fix this?

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

[kamoors]

EDIT:

There was an issue with the naming scheme for the new reactions, however, it did not change the fact that some reactions that had -1;1 stoichiometry were returned.

[rmtfleming]

The code in this function is straightforward to read. e.g. it may exclude an objective reaction https://github.com/opencobra/cobratoolbox/blob/master/src/analysis/exploration/findExcRxns.m

use findSExRxnInd or findStoichConsistentSubset

The latter is the best option for detecting external reactions. See tutorials here: https://github.com/opencobra/COBRA.tutorials/tree/master/reconstruction/recon2FBAmodel

On Thu, 12 May 2022 at 15:16, kamoors @.***> wrote:

I am currently manipulating a model to add a new compartment, so the structure looks like this:

[c] <-> [e] (new <->) [NewComp] (new <->) []

1. modified original EX reactions to be met[e] <-> met[NewComp] (instead of met[e] <-> [])
2. added a new EX reaction met[NewComp] <-> []

The problem is that for some when I add these reactions, SOME of the [e] <-> [NewComp] reactions appear in the output of FindExcRxns, despite them having [-1;1] stoichiometry. I double checked this both using the stoichiometry output of the FindMetsFromRxns function, and by inspecting model.S for those functions.

Does anyone have an idea what could be causing this and how to fix this?

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

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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 & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu

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