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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.
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How to edit a file of edge attributes
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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 »
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How to import attribute from a file
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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 »
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GML file w/ node coordinates
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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
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NetworkView after destroying network
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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 »
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List of visible nodes
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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 »
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Integrating Cytoscape into a Web Page??
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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 »
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error
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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 ?
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Broken link for Cytoscape tutorials?
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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 »
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Problem with the online tutorials
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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 »
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