Curators notes for BIOMD0000000927 seem to be mixed up with another model

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Temporary place for coordination of updating existing Biomodels

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Curators notes for BIOMD0000000927 seem to be mixed up with another model #88

Closed jonrkarr closed 2 years ago

jonrkarr commented 3 years ago

The SBML and SED-ML appear to be associated with Baker et al., where as the curators notes appear to be associated with Grigolon et al.

jonrkarr commented 2 years ago

Todo

[ ] Review the original article, curation notes, and SED-ML.
[ ] Discern whether curation notes and/or SED-ML needs to be corrected or swapped.
[ ] Commit any corrections to the SED-ML to the manual-fixes subdirectory of this repository. Describe any corrections to the curation notes here.

freiburgermsu commented 2 years ago

@jonrkarr The curation notes and figure reflect Figure 1b on page 4 of the Grigolon et al. paper.

How can I render the SED-ML file to determine whether it describes this proper figure? My executions of the COPASI file do not recreate the figures from either the curation or the paper.

jonrkarr commented 2 years ago

The SED-ML files can be opened with COPASI. But, the COPASI files are fine to use too because the SED-ML files are derived from the COPASI files.

freiburgermsu commented 2 years ago

The only figure that is generated from a Time Course task of the COPASI file Grigolon2018_fig1b.pdf matches neither any of the curation figures nor any figures from the paper.

I also receive this error when I load the SED-ML file into COPASI SED-ML loading error which suggests that the corresponding SBML file not accessible to the SED-ML file.

Are these files broken, or must a different COPASI task be run?

jonrkarr commented 2 years ago

I think everything is fine. I'm going to close this issue shortly once I explore the COPASI bug described below.

The COPASI file (Grigolon2018_fig1b.cps) does produce the plots in the curation notes. The plot is from a parameter scan.

The SED-ML file (Grigolon2018_fig1b.sedml) is also close to capturing these plots. The one exception is that COPASI (v4.30) has a bug which leads it to import the wrong number of steps of the repeated task (a number much bigger than 1000). I'm going to try this with the latest version of COPASI and see if an bug report still should be filed, or this has been fixed.

jonrkarr commented 2 years ago

The COPASI warnings are substantially reduced to just 1 in the latest version (4.35).

jonrkarr commented 2 years ago

The number of steps of the repeated task is also now imported correctly with COPASI 4.35. Thus, no error needs to be reported to COPASI.