how to import a Large size text file

[xiangs]

I'm new to Cytoscape and trouble to import large text file.my text
file have more than16000 nodes and 23370311 edges(size 1.5G).
i use macbook pro with i7cpu,8G memory.Also i have edited the
cytoscape.sh file and
change:
java -Dswing.aatext=true -Xss10M -Xmx8G -jar cytoscape.jar
cytoscape.CyMain -p plugins "$@"
then i ran cytoscape.sh->file->import->network from table.then wait
wait wait.cytoscape load file 3 days and looks like will not stop.oh
my gold.how can i import lage size text file?can cytoscape deal this
large size file.

another question:
i try to import a small size file(70M).load successful and the no
action,no network view.i had to click edit->create view then wait wait
wati,unfortunately no network visualization.then again edit->create
view and then again and then again.I gave up

have anyone successful like this.can you tell me how to use cytoscape
import large file and create view.many many many thanks.

[Scooter Morris]

Greetings,
Yes, I have successfully imported large networks (I don't think
I've ever imported 23M edges, though). If you want to give me a pointer
to your 70M file, I'm happy to investigate as to why you can't visualize
it. As I suggested previously, though, setting your java size to be
equal to the amount of memory you have is a very bad idea. The -Xmx
parameter is the heap size (the amount of memory Java can allocate for
data), not the total footprint. By setting the heap to 8G when you only
have 8G of memory, you are going to induce significant paging, which is
extremely slow on a macbook (or any laptop for that matter). On an MBP
with 8G, I would never recommend setting your heap to larger than 6G.
23M edges is a lot of edges, and I'm not sure any kind of visualization
is going to be useful. Is there a way to filter the edges down a little?

-- scooter

[Tim te Beek]

Hi Marco,

Not sure how it will respond to such large input files, but for delimited files input I've written an alternative input plugin: http://apps.cytoscape.org/apps/alternativetableimport

Let me know if it solves your problem, or if you run into trouble using this alternate import plugin.

Best,

Tim

On Saturday, October 20, 2012 12:34:10 PM UTC+2, Marco Baglivo wrote:

Hi all,

there are some news? i'm very interested.

I've imported a dot file of 19M but i have not output, "please wait..." indefinitely

[zeng...@gmail.com]

Hi Xiangs,

have you successfully solved your problem about importing large size text data by using cytoscape ,since now I come accross the same problem, can you give me some hint if you have got a success ,thanks so much!