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Description:
Open forum for discussing Cytoscape, asking questions, and suggesting new features.
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Cytoscape.js 2.0.0 release
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*
Cytoscape.js 2.0.0 <[link]> is now available. It has improved performance over Cytoscape Web, built-in support for touch devices, gesture support, core extensions, UI plugins, and an intuitive API modelled after jQuery.
We will continue to support Cytoscape Web for now, but we advise users that... more »
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Creating a simplified network
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Hello, Cytoscape experts! I built a network from importing physical interactions from web service and all interactions (edges) are two-way. Is there any way to simplify the network at all by collapsing all of these redundant undirected edges into a single undirected edge per pair of nodes? I would prefer finding a method... more »
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running sample bundle apps
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I keep getting this error when I try to run the sample apps in the cytoscape-sample-apps git: Cytoscape 3.0.1> start 171 org.osgi.framework.BundleExcep tion: Unresolved constraint in bundle sample09 [171]: Unable to resolve 171.0: missing requirement [171.0] package; (&(package=org.cytoscape.servi ce.util)(version>=3.1.0)(!(ver sion>=4.0.0)))... more »
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XGMML Linkout Example
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I have a simple XGMML network that I generated via a script and I'd like to
add linkouts to different sites. Does anyone have a simple example of a
single node with a linkout?
Regards,
Mark Fortner
PS a number of links on the XGMML wiki page are broken.
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Hierarchy of the type CyActivator is inconsistent
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Hi Victor,
That error happens when one of the super classes/interfaces can't be
resolved through the classpath. It's likely that your classpath is
incomplete. What error are you getting from Maven or your IDE?
Thanks,
Jason
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unselect all nodes
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Hi,
is there a way to unselect all the nodes of a network without
iterating on all the nodes?
(the old unselectall() method)
thank you!
--
Giovanni Scardoni
The Center for BioMedical Computing (CBMC)
[link]
University of Verona
Strada le Grazie, 15 -37134
Verona -Italy... more »
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dependencies cytoscape 3 app
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Hi All,
I'm working on a new cytoscape 3 app and recently, I added a new dependecy (lucene) to my pom file. However when I test the app jar in Cytoscape, the app fails to load. I had a look into the jar and apparently the dependencies are not exported, from that I conclude that I'm missing... more »
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Panzoom() - how to call properly ? (js)
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I have inside my read:function(){ var $container = $("#cytoscape"); // debugger; $container.cytoscapePanzoom(); ... ...on chrome console I see that I have the Panzoom div setted, but I cannot see the controls. Are there anything else I need to call to display the panzoom control for my graph ?... more »
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cy.on calling for each node selected (cytoscape js)
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I am trying to get all information from selected node in my graph (using cytoscape js) to build an information table (as I used to do with cytoscape web - flash version) but I don't find a way for doing it using the js version. (I am super new to jquery / javascript ). Trying to use this example:... more »
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Malformed Input When Loading a Network
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There's a particular network I've been trying to load on to Cytoscape all morning but to no avail. I can't seem to fix whatever's wrong because of this rather mystifying error message: *The task could not be completed because an error has occurred.* * * *java.nio.charset.MalformedInp utException: Input length = 1*... more »
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