Re: [Biomodels-net-support] SBML conversion - FBC package converter to SBML Level 2

[Nicolas Rodriguez]

Hi,

So the SBML to SBML conversions should be working again, could you give it a try ?

I did put Simon Lam in CC because he had the same problem as you some time ago,

Just a note in case, you are trying to convert a SBML L3 models that does contain the FBC package. The current converters won't be able to convert those but you could use either:

- the jsbml converters, documentation available at https://sbmlteam.github.io/jsbml/files/doc/api/1.5/org/sbml/jsbml/ext/fbc/converters/package-frame.html

- the libsbml converter, documentation available at http://sbml.org/Software/libSBML/5.18.0/docs/java-api/org/sbml/libsbml/FbcToCobraConverter.html

- they are also converters available in http://pysces.sourceforge.net/ and may be the cobra toolbox or cobrapy can do it as well.

Unfortunately, those pages are very hard to find doing a web search, I was not able to make them appear into the first few pages of different search I try (side remark for the SBML team may be something to work on on the long term)

I could directly had one of those conversions inside SBFC if the FBC package was detected in an SBML file and the user try to convert it to SBML Level 2. Although, there does not seems to be a clear consensus among the SBML team that this should be done by default on the generic SBML converter.

I could also just had some comments in the error return by SBFC to point to those converters if FBC was detected.

One potential problem is that those converters would work only on SBML files that contain only the FBC package. Another potential problem, the FBC package was created because the SBML level 2 representation of those models was not precise enough and could lead to different interpretation of the model, so may be we should not push to use software to understand only SBML Level 2

cheers,

Nico

On 22/01/2021 22:38, Nicolas Rodriguez wrote:

Hi,

I thought this error was fixed already, I will try to have a look at the server and fix things if needed before end of next week.

Thanks,

Nico

Le 20/01/2021 à 19:15, Geoffrey Yu a écrit :

Hello,

I was using EBI’s web server to convert an SBML L3V1 file to SBML L2V4 but this error occurred:

The converter SBML2SBML you asked for can not be found...

java.lang.ClassNotFoundException: org.sbfc.converter.SBML2SBML
	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:264)
	at org.sbfc.converter.Converter.convertFromFile(Converter.java:167)
	at org.sbfc.converter.Converter.convertFromFile(Converter.java:138)
	at org.sbfc.converter.Converter.main(Converter.java:305)

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