We need more (computational) dakka!
I’m super excited to finish the ‘computer lab’ section of my research space! Although we are primarily a wet lab, the sheer number of computational tools available to augment biological research is too important to not tap into. This has paid off in my early forays into AlphaFold protein interaction prediction, enabling us to discover an entirely new interface within the 53BP1-RIF1-shieldin complex that we validated through various methods (see Sifri et al 2023). Between AlphaFold and RoseTTAFold neural networks for protein folding and interaction prediction, automated image analysis software, and the wide array of genomics data analysis tools available, we’re going to need some computational muscle. And of course, day-to-day research also requires a good workhorse for figure construction, image analysis, and other lighter computational tasks. To achieve these aims, I present our three workstations, Shadowfax, Seabiscuit, and Rocinante!
Shadowfax is a Linux server with 4xA5000 24GB GPUs, an AMD Threadripper Pro, with 256GB RAM. It will be used for heavy duty AlphaFold and RoseTTAFold predictions and other bioinformatics tasks associated with image processing and genomics analysis.
Seabiscuit is a Windows workstation with an Intel 13500CPU and 16GB of RAM. It will be loaded with a number of software important for our workflow (ApE, Adobe creative suite, Office, Fiji, FACS etc) and eventually a webcam and headset for video conferencing.
Rocinante is an old horse that I took with me from Toronto. It's a Linux server with 2xRTX2080 Supers, an Intel 10920X CPU and 64GB of RAM. It'll work for lighter loads but this guy can still run!
I am discovering that the new crop of graduate student applicants all have strong foundations in both experimental biology and bioinformatics. I’m keen on trainees who can seamlessly transition between the two to discover exciting new biology.
P.S. I am very sad to report that nobody in the lab understood the name references…
