While I could load that into Cytoscape, that was already far too big to be able to do anything useful with. I used to work with a human PPI network of ~13000 nodes and ~15000 edges. I really urge you to do some preprocessing and pare the network down to something more manageable. It will just look like a horrible hairball. However, a network with 200,000 nodes and 230,000 edges is just too large to be able to manipulate in any useful way in a GUI. Now, try loading network.csv into Cytoscape and then load each of the node and edge attributes separately. Assuming you have access to a *nix machine, you can run: awk -F"," '' file.csv > The first thing you can try is to separate the network from the meta information. I have about 200,000 nodes and 230000 edges. col2 is source node, col1 and col3 are attributes for source node,col 4 is destination node, col5,col6,col7 are attributes for destination node, col8 until end are attributes for edge. My system has 500GB ram and then I changed Cytoscape.vmoptions file according to -Xms102400M but when I load my file, in task manager, the memory increased until 50GB and then Cytoscape crashed and again it threw the same error: :Java heap space.
I have a 7.4 GB csv file (about 1,500,000 reords) and when I tried to load it into the Cytoscape it throws an error :Java heap space.
#CYTOSCAPE 3 INCREASE MEMORY WINDOWS#
I installed Cytoscape 3.7.1 with java 1.8.0_191 in windows server 2012.
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