Issue Tracker Database is Down & SBML model not read anymore in 4.37 (Build 264)

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Matthias König

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Oct 20, 2022, 9:41:41 AM10/20/22
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Hi all,
I just tried to read the attached SBML model with the new COPASI release.
This fails with

Error while loading file /home/mkoenig/git/pkdb_models/pkdb_models/models/pravastatin/models/results/pravastatin_liver_cholesterol.xml!

>EXCEPTION 2022-10-20T15:38:12<

SBML (55): Could not find unit definition for unit with id "m2" used in "units" attribute of compartment with id "Vbaso".

Resulting in an empty model without objects.
- The model is valid SBML
- The model could be read with the previous COPASI version
There were some major bugs introduced with units support in the lastest COPASI version.

Model is attached.

I tried to report the bug, but the tracker database is down at

Software error: Can't connect to the database. Error: Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (111) Is your database installed and up and running? Do you have the correct username and password selected in localconfig?

Best Matthias
pravastatin_liver_cholesterol.zip

Hoops, Stefan (sh9cq)

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Oct 20, 2022, 10:53:26 AM10/20/22
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Hello Mathias,

Thanks for reporting both issues. The database has been restarted and
the tracker is running again. I will look into the issue.

Thanks,
Stefan

On Thu, 2022-10-20 at 06:41 -0700, 'Matthias König' via COPASI User
--
Stefan Hoops, Ph.D.
Research Associate Professor
Biocomplexity Institute & Initiative
University of Virginia
995 Research Park Boulevard
Charlottesville, VA 22911

Phone: +1 540 570 1301
Email: sho...@virginia.edu

Hoops, Stefan (sh9cq)

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Oct 20, 2022, 11:11:28 AM10/20/22
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Hello Mathias,

The error message is misleading and should only be a warning. COPASI
stumbles over the use of an area unit m^2 for a 3 dimensional
compartment basolateral membrane (VBaso). Correct the dimension of your
compartment and you should be fine.

Thanks,
Stefan

Matthias König

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Oct 20, 2022, 12:04:11 PM10/20/22
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Thanks Stefan. This fixed the issue with model loading and improved the model ;)

The old COPASI Version 4.36 had no issue with the spatialDimensions and read the model without issue. I always thought the spatialDimensions are mainly for annotation, but do not have meaning for the actual math/model. So it is strange that this results in the model not being loaded in the new version 4.37.

Best Matthias

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--
Matthias König, PhD.
Junior Group Leader Systems Medicine of the Liver Lab
Humboldt-Universität zu Berlin,
Institute of Biology, Institute for Theoretical Biology
Philippstraße 13, Haus 20, 10115 Berlin
Tel: +49 30 2093 98435

Hoops, Stefan (sh9cq)

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Oct 20, 2022, 12:17:43 PM10/20/22
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Hello Mathias,

The check for appropriate units has been improved however an incorrect
message was generated. This will be fixed in the next release.

Thanks,
Stefan


On Thu, 2022-10-20 at 18:03 +0200, 'Matthias König' via COPASI User
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