search

opencobra / cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
https://opencobra.github.io/cobratoolbox
Other
241 stars 305 forks source link

bug in writeSBML line 496 #2122

Open maziya opened 1 year ago

maziya commented 1 year ago

defaultSboTerm is not defined in line 496 of writeSBML function. It should be set as defaultSboTerm = 176

I hereby confirm that I have:

(Note: You may replace [ ] with [X] to check the box)

rmtfleming commented 1 year ago

Fork, fix, PR.

On Mon, 5 Jun 2023 at 11:33, maziya @.***> wrote:

defaultSboTerm is not defined in line 496 of writeSBML function. It should be set as defaultSboTerm = 176

I hereby confirm that I have:

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

(Note: You may replace [ ] with [X] to check the box)

— Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/2122, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAQMEOWPL5XS44MLLHSJLVDXJWYXJANCNFSM6AAAAAAY2YVDU4 . 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 & Coordinator of the Horizon Europe project "Reconstruction and Computational Modelling for Inherited Metabolic Diseases" (Recon4IMD)

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.)

tpfau commented 1 year ago

Which version of the toolbox are you running? Line 496 of writeSBML has to do with confidence scores, (and been so for quite some time). Also for reactions the defaultRxnSboTerm is set to 176 in line 481, so I'm not sure what you are referring to.

maziya commented 1 year ago

Which version of the toolbox are you running? Line 496 of writeSBML has to do with confidence scores, (and been so for quite some time). Also for reactions the defaultRxnSboTerm is set to 176 in line 481, so I'm not sure what you are referring to.

My apologies. I have now updated the toolbox.