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Description: This is a list for asking questions about and getting help with Cytoscape (http://cytoscape.org).   We encourage ALL users to post ANY questions they might have related to the use of Cytoscape.

 

How to edit a file of edge attributes 
  I am a new user of cytoscape. I edited a file of node attributes: primarykey alias expressionstrength a1 b1 0.3 a2 b2 0.4 a3 b3 0.5 The format is .xls.Then I imported the file sucessfully.But I came across some problems when I tried to import a file of edge attributes:... more »
By betty  - Nov 21 - 2 new of 2 messages    

How to import attribute from a file 
  Here is the case:I import a network from the table,but come across a prolem when I try to import the edge attribution from the file ***.eda.For example,I importe the following network: a1 pp a2 a2 pp a3 a3 pp a1 a3 pp a3 the fomat of the file above is .xls. Then I try to import the edge attribution from the file ***.eda.The... more »
By betty  - Nov 18 - 6 new of 6 messages    

tutorial pages are down 
  [link] leads to "internal server error"
By zikester  - Nov 16 - 2 new of 2 messages    

GML file w/ node coordinates 
  Hey, I have a GML file w/ 12682 nodes and 14703 edges. when importing in yEd all works fine. but when I try to import it into cytoscape the coordinates are NOT displayed properly (node and edge cardinal is correct). what happened? thanks johannes
By Johannes  - Nov 15 - 4 new of 4 messages    

NetworkView after destroying network 
  Hi, I have a PropertyChangeListener listening for Cytoscape.NETWORK_DESTROYED events. When I destroy an empty network directly after creating it in a new session, Cytoscape.getCurrentNetworkVie w() returns a FingCyNetwork (not the one returned by Cytoscape.getNullNetworkView() ). Hence, MyCytoscapeAction.enableForNet workAndView() enabled the... more »
By gregor.warsow@uni-greifsw ald.de  - Nov 15 - 7 new of 7 messages    

List of visible nodes 
  Hi, is there a way to be informed about nodes leaving the visible area of the network view (by zooming in or sliding the network) or to get a list of the nodes being currently visible? (One could describe those nodes out of scope as hidden nodes, but I am not interested in nodes that have been hidden by the user [CTRL+H]).... more »
By gregor.warsow@uni-greifsw ald.de  - Nov 12 - 1 new of 1 message    

Integrating Cytoscape into a Web Page?? 
  Hi, I'm an Italian student, currently I use cytoscape for build cooccurrent protein network but I would also integrate(construction and visualization of networks)cytoscape in a web application(only in a web page), is it possible? I try to search information and read wiki,for example I think that... more »
By Marco  - Nov 11 - 4 new of 4 messages    

error 
  hi, when i enter web services and enter the pathway details and show interaction of particular gene.., then error comes.."see log for details" wht should i do ?
By Reshmi Suresh  - Nov 9 - 4 new of 4 messages    

Broken link for Cytoscape tutorials? 
  Hi folks, Greetings from Argentina, where I'm on sabbatical for a couple of months... I just received a lovely, polite email from someone who apologized for contacting me while I'm away, but was desperately trying to get to the Cytoscape tutorials. At the moment, the link from cytoscape.org appears to be broken. Would someone do the honors... more »
By Melissa Cline  - Nov 4 - 1 new of 1 message    

Problem with the online tutorials 
  Hi, I'm a PhD student, currently learning to use cytoscape but I have a problem with the online tutorials. Everytime I try to open the tutorials I receive the following message " Internal Server Error The server encountered an internal error or misconfiguration and was unable to complete your request.... more »
By Shady Saad  - Nov 3 - 3 new of 3 messages    

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