Question: KEGG CONVERTER - KGML to SBML
0
gravatar for me.sr1510
3 months ago by
me.sr15100
me.sr15100 wrote:

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

software error • 213 views
ADD COMMENTlink modified 3 months ago by draeger0 • written 3 months ago by me.sr15100
0
gravatar for mhucka
3 months ago by
mhucka50
California Institute of Technology
mhucka50 wrote:

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/ ?

ADD COMMENTlink written 3 months ago by mhucka50

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

ADD REPLYlink written 3 months ago by me.sr15100

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

ADD REPLYlink written 3 months ago by mhucka50
0
gravatar for draeger
3 months ago by
draeger0
draeger0 wrote:

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?

ADD COMMENTlink written 3 months ago by draeger0
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