Why is rxn.mat loaded in neighborRxn2data

[akaviaLab]

https://github.com/opencobra/cobratoolbox/blob/c72a7bd511f79ebc1b6b1e0421544b22b4a9335d/src/reconstruction/rBioNet/neighborRxn2data.m#L44

This is unclear, since it loads up existing data, instead of using the model. Was this perhaps meant to be "rxns"?

[akaviaLab]

rxn.mat is a small matrix distributed in src/reconstruction/rBioNet/rxn.mat and in cobratoolbox/test/verifiedTests/reconstruction/testRBioNet/ which seems to bias the functions of rBioNet. ping @laurentheirendt, @rmtfleming, since I believe you guys wrote rBioNet.

[rmtfleming]

Hi, I think rxn.mat is a set of reactions. It is assumed that it is in the current folder or a folder in the current path. Perhaps the code could be edited to select a path to a rxn.mat. Regards, Ronan

https://github.com/opencobra/cobratoolbox/blob/c72a7bd511f79ebc1b6b1e0421544b22b4a9335d/src/reconstruction/rBioNet/rxn.mat

On Mon, 10 Jun 2019 at 14:28, akaviaLab [email protected] wrote:

rxn.mat is a small matrix distributed in src/reconstruction/rBioNet/rxn.mat and in cobratoolbox/test/verifiedTests/reconstruction/testRBioNet/ which seems to bias the functions of rBioNet. ping @laurentheirendt https://github.com/laurentheirendt, @rmtfleming https://github.com/rmtfleming, since I believe you guys wrote rBioNet.

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

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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