BioNetBuilder setup

[seema]

How to place the properties file in cytoscape top directory? The properties file is just a string of some text. What to name it when copy-pasting in a notepad?  Also, cytoscape version is 2.8.3. BioNetBuilder wizard says unable to create bionetbuilder wizard. Kindly let me know what to do. Thanks.

[Kevin Drew]

Hi,

With the new cytoscape versions, you manage the plugins through the
Plugins->Manage Plugins panel. Is this how you installed
BioNetBuilder? If so, it might be worth uninstalling and reinstalling
the plugin. Also, check and see if Plugins->Set BioNetBuilder
Connection has the correct url: http://err.bio.nyu.edu/bionetserver2

Thanks,

Kevin Drew
Bonneau Lab

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[seema]

Thanks, Kevin. I have a proxy setup. I have let cytoscape know about this proxy number through edit-preferences menu. Still BioNetBuilder is not getting connected to network. For installation, I just put in the Bionetbuilder .jar file in plugins directory of cytoscape. Just let me know how to use manage plugins command to install bionetbuilder. I have a proxy server for internet. I tried to use manage plugins and it gives error below. Please let me know how to install correctly. Thanks, Seema.
cytoscape.actions.

PluginManagerAction$ManagerAction[ERROR]: Failed to get input stream for "http://cytoscape.org/plugins/plugins.xml"! Caused by: Failed to get input stream for "http://cytoscape.org/plugins/plugins.xml"! at cytoscape.util.URLUtil.getBasicInputStream(URLUtil.java:109) at cytoscape.util.URLUtil.getInputStream(URLUtil.java:68) at cytoscape.plugin.PluginFileReader.(PluginFileReader.java:49) at cytoscape.plugin.PluginManager.inquire(PluginManager.java:326) at cytoscape.plugin.PluginManagerInquireTask.run(PluginManagerInquireTask.java:77) at cytoscape.task.util.TaskWrapper.run(TaskManager.java:160)

[Kevin Drew]

Hi,

This sounds like it is a problem with your proxy.  I would contact your system administrator that set up the proxy.

Thanks,

Kevin

[Kevin Drew]

Hi Peter,

Sorry for the trouble.  The server BioNetBuilder runs on is slowly dying and unfortunately there are no plans to replace it.  I will try to get the server up and running again so you can use it but it probably is not a long term solution for you. 

Another option might be to use the GeneMania website which also has a cytoscape plugin. 
http://www.genemania.org/

Again sorry for the trouble,

Kevin Drew

Marcotte Lab

On Tue, Oct 15, 2013 at 9:08 AM, <pbaa...@xs4all.nl> wrote:

Dear Kevin,

 

I have been able to retrieve PPI data for Streptococcus species using Bionetbuilder, however today I do not appear to be able to do so. Is there a change in the organisms included in Bionetbuilder, or a database communication error?

 

all the best, Peter 

[Kevin Drew]

Hi,

The BioNetBuilder server is back up and running.  Again, we cannot offer any guarantees about its uptime.

Thanks,

Kevin