Use PSICQUIC in another Cytoscape app

[k.gra...@gmail.com]

Hello,

I am currently working on a student project and I have to automatically collect protein-protein interactions from multiple databases then visualize these PPi with Cytoscape 3. So I would like to use PSICQUIC to get such data into my own Cytoscape app.

It seems that the Cytoscape 3 API does not allow programmers to use the implemented PSICQUIC client (or at least, I did not succeed).

My question is: is it possible to use the PSICQUIC client implemented in Cytoscape 3, and how? Or should I use the Java client?

Thank you so much for your help.

[Marine Dumousseau]

Hello,

You should refer to the cytoscape helpdesk and discussion group first, they are very active and responsive and may explain why you cannot use the implemented PSICQUIC client:

http://groups.google.com/ group/cytoscape-helpdesk/ topics and http://groups.google.com/ group/cytoscape-discuss/topics.

If they cannot help you with cytoscape 3 PSICQUIC plugin, you can give me more details about your pipeline and I may be able to help you with our PSICQUIC client.

For the PSICQUIC services that can provide XGMML, you can download the results of your query in XGMML format and then import your files directly in cytoscape 3. For the other PSICQUIC services, you will need to convert MITAB to XGMML first unless cytoscape 3 can load MITAB files...

Cheers,

Marine

On Monday, December 9, 2013 2:52 PM, Pablo Porras <ppo...@ebi.ac.uk> wrote:

Hi,

I think, as a general rule, that he might be having problems with the 3.0 implementation due to the mistakes Kei was trying to fix. In any case, I don't think I can answer this question, please refer him to http://groups.google.com/ group/cytoscape-helpdesk/ topics and http://groups.google.com/ group/cytoscape-discuss/topics. They get lots of questiosn liek that and they are usually really helpful and responsive.

Cheers,

Pablo.

On 06/12/2013 16:59, Marine Dumousseau wrote:

Hi Pablo,

I forward you this user question because I think you will give a better answer about cytoscape 3 and the PSICQUIC plugin than me.

Cheers,

Marine

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Pablo Porras Millán, Ph.D.
IntAct Scientific Curator
European Molecular Biology Laboratory
European Bioinformatics Institute (EMBL-EBI)
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