ModelPolisher

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Unlike expected, the render specification seems to specify the `GlobalRenderInformation` class to use a `renderInformation` tag, possibly because it derives from the `RenderInformation` tag. (Section 3.5.3) https://raw.githubusercontent.com/combine-org/combine-specifications/main/specifications/files/sbml.level-3.version-1.render.version-1.release-1.pdf However, after application...

Schmoho

We actually have a test for this specific behaviour: https://github.com/draeger-lab/ModelPolisher/blob/113b46764b2df15a0333e6a1244fa1215cee7c39/lib/src/test/java/de/uni_halle/informatik/biodata/mp/fixing/fbc/ListOfObjectivesFixerTest.java#L99C1-L117C6 Evaluation of cobrapy validator results for the Biomodels dataset however revealed this yields a COBRA_WARNING. This behaviour can be seen...

Schmoho

This occurs on model https://www.ebi.ac.uk/biomodels/BIOMD0000000807 The error is very serious since it changes the mathematical interpretation of the model. This method https://github.com/draeger-lab/ModelPolisher/blob/113b46764b2df15a0333e6a1244fa1215cee7c39/lib/src/main/java/de/uni_halle/informatik/biodata/mp/polishing/SpeciesPolisher.java#L84-L103 has two errors: 1. It interprets the species...

Schmoho

Can be observed on model https://www.ebi.ac.uk/biomodels/MODEL2308220001 where this annotation exists: ```xml [...] ``` (chemspider and hmdb annotations) MP truncates this, so the whitespace is gone. cobrapy does not recognize the...

Schmoho

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1

Hi, I was looking to install your software through docker, so I ran: ``` $ docker search ModelPolisher NAME DESCRIPTION STARS OFFICIAL mephenor/modelpolisher 0 schmirgel/modelpolisher 0 schmirgel/mpserver Server Implementation for...

IlFog

We are currently supporting SBML 3.1 in our code, but this is never handled explicitly. Proper support for 3.2 and 2.X versions suggests we restructure the code s.t. fixing/polishing/annotation modules...

Schmoho

Hi, I have a docker error : ``` WARNING: Some services (validator) use the 'configs' key, which will be ignored. Compose does not support 'configs' configuration - use `docker stack...

lcottret