SBML import

[Alex]

Apologies if the answer is simple.

I have downloaded Cytoscape version 2.2. When I try to import KEGG SBML

pathways, the susequent network just has nodes but no edges. Where am I

going wrong?

Thanks,
Alex

[Rowan Christmas]

what plugin are you using to import? mine?

[Alex]

Yes, SBMLParser.jar

[Rowan Christmas]

you need to pass -sbml <filename> when starting cytoscape

On 1/12/06, Alex <alexandra....@gmail.com> wrote:
>

> I can't seem to find an option for the SBML import in the plugins or
> file--load menu. Is it
> glaringly obvious? Or, is the plugin automatically executed when
> loading in an XML file?
>
>

[Alex]

I carried this out and the network loaded still has no edges.
It is loading the network, and the node names are correct,
just no edges.

Alex

[Alex]

Rowan, just a question,
Do you have the SBML parser plugin visible in your plugin menu
when using the software? Or, is it in the file>load menu? Or, is
it just automatic?

[Rowan Christmas]

I'll have to check, I think it might be under the "SBML" menu.

Where is your SBML file coming from? is it from systems-biology.org?
or are you making it yourself?

I have not used SBML all that much so it may be that the way I am
parsing the edges is too dependent on the KEGG semantics. If this is a
SBML file not made from KEGG using kegg2sbml then I might need to take
out some semantics to get it to work properly.

[Alex]

The SBML file is your example from a previous thread (Import and
export of SBML) and KEGG files from systems-biology.org.

I can't see a SBML menu on this version of Cytoscape that I have.

Are there any additional things I need perhaps?