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sys-bio / temp-biomodels

Temporary place for coordination of updating existing Biomodels
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Correct non-zero SED-ML output start times #94

Closed jonrkarr closed 2 years ago

jonrkarr commented 3 years ago

COPASI SED-ML export ignores output start times.

In some cases (e.g., BIOMD0000000794), this leads to very different results.

jonrkarr commented 3 years ago

COPASI bug filed as http://tracker.copasi.org/show_bug.cgi?id=3046

freiburgermsu commented 2 years ago

@jonrkarr The original bug post, on the COPASI forum link, seems to have been resolved within the past few weeks. Is this still an actionable item for curation, or was it only a COPASI bug? If the former, would the best approach be to devise a script that identifies and corrects all of the models that contain this edge case?

jonrkarr commented 2 years ago

It looks like the correction to COPASI will be released with 4.35, which hasn't been released yet. Once this is released, COPASI could be used to re-generate the SED-ML files. @luciansmith previously used COPASI to generate SED-ML files and could do it again.

luciansmith commented 2 years ago

It's actually part of the pipeline, so as soon as 4.35 is out, all we need to do is run the pipeline again.

jonrkarr commented 2 years ago

@luciansmith 4.35 is out. Can we correct this?

luciansmith commented 2 years ago

Looks like 794 is indeed corrected with the latest COPASI, so yes!