minimum specs to use Cytoscape

[Afiqah Aleng]

Hi,

I am having a problem to do any analysis of a network (20,000 proteins with 500,000 interactions) in Cytoscape. My computer always stuck when I want to load the network into Cytoscape. I am planning to buy a new computer. Can anyone suggest the minimum specs of a laptop to run that huge network in Cytoscape smoothly?

I hope anyone can help me in this problem. 

Thanks in advance,

Afiqah

[Barry Demchak]

Hi --

This shouldn't be a problem for a modern PC ... are you using a 32 bit machine right now? That might be the first issue.

If you're using a 64 bit machine now, are you sure you have the 64 bit JVM and 64 bit Cytoscape installed? 

It might be helpful for you to run the Troubleshooting script (http://cytoscape.org/troubleshooting.html) and post the results here. If you're running Windows, be sure to save the script on your disk and then run it from a command line.

Also, if you're willing to send me your network, I can try it on one of  our machines.

Note that the minimum requirements for Cytoscape are modest (http://manual.cytoscape.org/en/stable/Launching_Cytoscape.html#system-requirements) ... the issue is how large a configuration do you need for the network you're interested in.

Note, too, that Cytoscape 3.2 and later makes better use of its memory ... if you're not using latest Cytoscape (3.4), you should consider upgrading.

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpdesk+unsub...@googlegroups.com.
To post to this group, send email to cytoscape-helpdesk@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
For more options, visit https://groups.google.com/d/optout.

--

vvvvvvvvvvvvvvvvvvvvvvvvvvvv
: Barry Demchak, PhD
: UC San Diego, Department of Medicine
: https://sosa.ucsd.edu/confluence/display/~bdemchak/Home
: (858) 452-8700
vvvvvvvvvvvvvvvvvvvvvvvvvvvv