Opening gml files on a Mac

[DaveC]

Hi;

I have a simple network of 68 genes, originally created in cytoscape 1,
labels are refseq ids. I can open this on my linux box with cytoscape
2.1, I get the expected number of nodes.

If I try to open this using cytoscape 2.1 on a mac, it only loads 18
nodes. When browsing to find the network.gml file, only files with the
extension .sif are recognized, so I've been renaming the file
network.sif.

1) Does the extension influence how the file is interpreted?
2) why won't the mac version recognize .gml files?
3) Can I save the network as a .sif file from cyto 2?

Thanks.

[Rowan Christmas]

the Mac file browser is somewhat strange, but it should be finding
both sif and gml files. Are the 18 nodes it is finding correct, or do
they have strange names that would suggest the file is loading
incorrectly?

[DaveC]

Sorry, too much of a neophyte to tell. The nodes have no visible
labels, and the only way I've found to display these is to use the
'collapsing_biomodules_view' visual style.

I went back to the network on linux and did File->Save->Network as
interactions, and saved it as filename.sif. I could then find it in
the mac-cyto file browser and opened it up - this found the expected 68
nodes. These nodes didn't display their 'labels' either, even with the
above mentioned visual style.

A dirty secret about this 'network', is that it isn't - rather it is
simply a list of genes of interest that I hoped to bootstrap into a
network using the 'fetch interactions' plugin. Thus the .sif file that
linux-cyto created and I loaded was simply a list of names.

In my experience, on two separate macs running OSX 10.2(ish), is that
the File->Load->Network ignores both .gml and .GML files, but sees .sif
files.