The International Conference for High Performance Computing, Networking, Storage, and Analysis
The International Conference for High Performance Computing, Networking, Storage, and Analysis
Workshop: The 17th Workshop on Workflows in Support of Large-Scale Science (WORKS22)
Authors: Tomasz Osinski (University of Southern California (USC)); Mats Rynge and Karan Vahi (University of Southern California, Information Sciences Institute); James Hong, Ruilin Chu, and Cesar Sul (University of Southern California (USC)); Ewa Deelman (University of Southern California, Information Sciences Institute); and Byoung-Do Kim (University of Southern California (USC))
Abstract: Cryogenic electron microscopy (Cryo-EM) is a method applied to samples cooled to cryogenic temperatures that can reach a near-atomic resolution of biological molecules. Recent progress in methodology has created an entirely new set of challenges to overcome - among them, the specific environment of the HPC system and coordination and automation of the initial stages. Our solution is an automated Cryo-EM image pre-processing service tailored to an HPC environment with close to real-time feedback allowing the researchers to interact with the data acquisition session located in a facility remote to the HPC cluster. We automated the data transfer, created a service around the Pegasus Workflow Management System, kept the user interaction minimum, and offered the researcher an option to start the pre-processing right after initiating the microscope session. The users receive real-time feedback enabling them to interact with the data acquisition, adjust it and collect a better dataset.
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