Folding@Home and Genome@Home: Using distributed computing to tackle previously intractable problems in computational biology

TL;DR

This paper discusses how distributed computing enables tackling complex biological problems like protein folding that were previously computationally infeasible, highlighting methods, challenges, and data analysis issues.

Contribution

It introduces the use of distributed computing for large-scale biological simulations and addresses associated challenges in computation and data analysis.

Findings

Distributed computing breaks previous computational barriers in biology.

Efficiently dividing complex calculations across many PCs is feasible.

Handling and analyzing large simulation data remains a significant challenge.

Abstract

For decades, researchers have been applying computer simulation to address problems in biology. However, many of these "grand challenges" in computational biology, such as simulating how proteins fold, remained unsolved due to their great complexity. Indeed, even to simulate the fastest folding protein would require decades on the fastest modern CPUs. Here, we review novel methods to fundamentally speed such previously intractable problems using a new computational paradigm: distributed computing. By efficiently harnessing tens of thousands of computers throughout the world, we have been able to break previous computational barriers. However, distributed computing brings new challenges, such as how to efficiently divide a complex calculation of many PCs that are connected by relatively slow networking. Moreover, even if the challenge of accurately reproducing reality can be conquered, a new challenge emerges: how can we take the results of these simulations (typically tens to hundreds of gigabytes of raw data) and gain some insight into the questions at hand. This challenge of the analysis of the sea of data resulting from large-scale simulation will likely remain for decades to come.