Cytoscape - disproportionately big files

Question

[boczniak767]

Hi all,

I tried to get rid of most networks in my cytoscape file to make it load faster. I deleted 80% of networks in file and saved it.

And now I have this new file which is larger than original (new=135Mb, old=102Mb).

So my operation have absolutely reverse result.

Anyone, has similar problem? Is it better to export desired networks (which format?) and make new cytoscape file with imported networks?

Whad do you think?

[boczniak767]

Thanks, that somehow make sense but after all

less networks=less information=less information to compress.

Anyway, the other problem is that Cytoscape opens this file for forever... Even on machine with eight cores and 96 RAM. Cytoscape also don't use all computational power during opening, and SSD disk don't help here.

[xanderpico]

Just a note about an alternative way to reduce .cys files. You can rename them .zip, open them up and remove individual networks (xgmml files), etc., then rezip, and rename. I'd recommend doing this on a copy of your original .cys so you don't permanently wreck an important file :)

[boczniak767]

I tried, in linux renaming file is not necessary but xgmml files have numeric names and it is not possible to identify which corresponds to a given network. There are also more xgmml files than networks. Maybe I have buggy Cytoscape installation so deleted networks in fact remains in the file making it big - just a quess.

Answer 1

[Jean-Karim Heriche]

Most likely this has to do with compression. Compression doesn't always reduce file size. Compression typically makes use of redundant information. By removing networks, some information that was redundant may not be anymore and thus harder to compress.