ntamas / cl1 Goto Github PK

Link: http://trove.starlight-systems.com/

Thank you so much for this valuable project, I have been trying to run the project for a couple days, but I couldn't figure out how to do it, since I have less experience with java projects. I hope someone can explain how I can get the project compiled and running. I have gone through the command line folder, it says to run a command with a jar file, but I can't find it anywhere.
Thank you so much

Hi All,

I was trying to run ClusterOne with a graph with edges list file of size ~4.5GB, but the program throws a heap space limit error.
I tried to fix that by setting the maximum size of the heap "-Xmx10000M" (give it a 10GB memory), but it still crushes.
Any idea how to solve this problem?

Once the app is uninstalled, the menu item wouldn't go from "Apps" menu unless Cytoscape is restarted

E.g., let us assume the following two vectors:

xs = [4,4,4,4,4,4,4,4,4,4,4,6]
ys = [1,1,0,0,0,0,0,0,0,0,0,0]

R and SciPy seem to apply a different form of tie correction and not the one used by ClusterONE, therefore the results are a bit different. Also, judging from SciPy's source code, the sign of the continuity correction might also be different. Check the implementations of R and SciPy to see if we can make ClusterONE consistent with them.

SciPy's implementation:
https://github.com/scipy/scipy/blob/v0.11.0/scipy/stats/stats.py#L3447

The tie correction part of SciPy is implemented in C so we have to dig a bit deeper:

Hi!

I was wondering how to make ClusterONE run in parallel for multiple cores? I noticed that a recent bug fix pertained to multithreaded execution, but there seems to be no official documentation on how to do that. Is it for the command line version only? Or is it available in the cytoscape version too?

Any help would be appreciated :)

Has this option(Extract selected clusters) worked for you before ?

Simple fix would be changing this..

NewNetworkSelectedNodesAndEdgesTaskFactory taskFactory = this.resultViewer.getCytoscapeApp().getService(CySwingAppAdapter.class).get_NewNetworkSelectedNodesAndEdgesTaskFactory();

I've tested this, Shall I send a PR ?

I took a peek at the build.xml file and I suspect this is due to the app being built on Java 5 (https://github.com/ntamas/cl1/blob/master/build.xml#L41). This is now so old that some basic things just don't work anymore.

Any developers available to attempt building an updated version of the app and to submit to the Cytoscape App Store?