Regarding Bundling of large-sized networks

[Drishtee Barua]

Hello,

I have been trying to construct a Transcription factor- Target gene regulatory interaction network, the input file for which has a size of approx 100-200 MB. I allocated 90 GB of memory for usage of Cytoscape software, but the system still keeps hanging during the process of Bundling edges of the network file.

I have a 64-bit system of 64GB RAM, 4TB disk capacity running on ubuntu 20.04 LTS.

Any suggestions regarding how to continue the Bundling process for large-sized input files would be very helpful.

Thank you.

[Alex Pico]

Ah, you've found one of the most inefficient functions in all of Cytoscape! Seriously, "bundle edges" is high on our list to rewrite for efficiency. It barely works on medium size networks. It simply won't work with large networks. The fix is not simple, but we are aiming for a replacement for 3.10 (Q2 2022 or later).