KEGG CONVERTER - KGML to SBML

Question

[me.sr1510]

hi everyone,

I have to make the KEGG pathway downloaded in form of KGML compatible to cell designer for model building. As per my information I have to convert it to SBML. I searched and found KEGG Converter software which can be used for this purpose. I have been trying to use it but i m getting following errors:

Input for convertion: 2 kegg files. Output directory 'out/' is empty for the new results: true ERROR: 'Connection timed out (Connection timed out)' ERROR: 'com.sun.org.apache.xml.internal.utils.WrappedRuntimeException: Connection timed out (Connection timed out)' Error at converting file in/hsa04151.xml, count:0 javax.xml.transform.TransformerException: javax.xml.transform.TransformerException: com.sun.org.apache.xml.internal.utils.WrappedRuntimeException: Connection timed out (Connection timed out)

Kindly help me solve these errors. Moreover apart from KEGG Translator, and KEGG converter if there are any better tools for this purpose Please let me know

Thank You

Answer 1

[mhucka]

Hi,

You didn't mention which KEGG translator you are trying to use. I'm aware of at least two. Are you using the one at http://www.cogsys.cs.uni-tuebingen.de/software/KEGGtranslator/ ?

[me.sr1510]

YeSS that's the one I m talking abt....

[mhucka]

I've alerted one of the developers. Hopefully someone will get in touch with you.

Answer 2

[draeger]

Could you please state which software was used (KEGGtranslator or KEGGconverter)? Please also note that CellDesigner can only import SBML up to Level 2 Version 4. This is important when saving your result. About the timeout: are you behind a proxy that blocks connections?