Regarding using bridgedb services with Cytoscape 3.0

[tanisha]

Hi,

I am building a Cytoscape 3.0 app and need to use bridgeDB for connecting to wikipathways. But I am not sure how to proceed with the same. It would be great if anyone could guide me through the same.

Regards,
Tanisha

[Martijn van Iersel]

Hi Tanhisha,

I haven't done this yet myself. All I know is that the current BridgeDb
bundles are proper OSGi bundles so in theory it should work well with
Cytoscape 3.0.

Alex, have you worked on this yet?

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[Mike Smoot]

Here's a sample 3.0 app that depends on third party bundles.  The result is a something called a "kar" file, which stands for Karaf Archive.  It is just a jar file that contains OSGi bundles and a features.xml file that tells Karaf (the OSGi launching engine Cytoscape uses) to load all of the bundles.  

The sample app depends on some JFreeChart bundles, but in your case you would just depend on the various BridgeDB bundles that you need.  

Once you've got the kar file, you can copy it into the deploy directory and it should start.  The Cytoscape App Store does not yet support kar files, but that's something we're working on as it is an important feature for several projects.

thanks,

Mike

On Thu, Aug 2, 2012 at 4:05 AM, Martijn van Iersel <mvani...@gmail.com> wrote:

Hi Tanhisha,

I haven't done this yet myself. All I know is that the current BridgeDb bundles are proper OSGi bundles so in theory it should work well with Cytoscape 3.0.

Alex, have you worked on this yet?

--
Martijn

On 02/08/12 11:49, tanisha wrote:

Hi,

I am building a Cytoscape 3.0 app and need to use bridgeDB for
connecting to wikipathways. But I am not sure how to proceed with the
same. It would be great if anyone could guide me through the same.

Regards,
Tanisha

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[immortal meluha]

Hi Mike, Martijn,

I am sure BridgeDb would work fine with my app. But I am not able to connect to WikiPathways using BridgeDB library. Earlier, with pathvisio and BridgeDb this was possible and I worked out those examples sometime back, but now when I am don't know how could I import classes for wikipathways client.

Regards,
Tanisha

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[Martijn van Iersel]

Hi Tanisha,

WikiPathways and BridgeDb are separate projects. If you want to use
WikiPathways, you should obtain the client code here:
http://www.wikipathways.org/index.php/Help:WikiPathways_Webservice


--
Martijn

On 03/08/12 11:51, immortal meluha wrote:
> Hi Mike, Martijn,
>
> I am sure BridgeDb would work fine with my app. But I am not able to
> connect to WikiPathways using BridgeDB library. Earlier, with pathvisio
> and BridgeDb this was possible and I worked out those examples sometime
> back, but now when I am don't know how could I import classes for
> wikipathways client.
>
> Regards,
> Tanisha
>
> On Thu, Aug 2, 2012 at 8:55 PM, Mike Smoot <mike....@gmail.com
> <mailto:mike....@gmail.com>> wrote:
>
> Here's a sample 3.0 app

> <http://chianti.ucsd.edu/svn/core3/samples/trunk/sample28/> that

> https://groups.google.com/d/__msg/bridgedb-discuss/-/__SMLOQlT8zZgJ
> <https://groups.google.com/d/msg/bridgedb-discuss/-/SMLOQlT8zZgJ>.

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