Cryo-EM is a Classic HPC Use Case

With large Data Sets, the need for GPU Acceleration, and Parallel Filesystems for High Performance Storage, Cryo-EM is rapidly growing along with its compute and storage requirements.  Many pieces of the core facilities are becoming more data-intensive as well.

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Cryo-EM is becoming the gold standard for high resolution protein structures.  This technique is where scientists flash freeze their sample down to cryogenic temperatures then place that tiny piece of ice under a cryogenic electron microscope and use a GPU to get a 3D reconstruction of the biomolecules from the sample.  Great work is being done with Cryo-EM and structural biology today especially surrounding the novel coronavirus and the search for a cure.  Researchers take thousands of 2D digital images of the ice scan to create a 3D reconstruction model and this is how we know what COVID-19 looks like all the way down to the molecular level.  Materials Science and Nanotechnology are also growing users of Cryo-EM and other forms of electron microscopy.

HPC for Cryogenic Electron Microscopy (CRYO-EM)

We know that solving molecular structures requires intensive computational and storage resources.  There are common IT challenges in the field that have proven the underlying IT infrastructure for Cryo-EM are as mission critical as the microscopes themselves, organizations need to maximize the utilizations and productivity of their equipment and associated resourced.  ComnetCo with HPE hardware and NVIDIA GPUs can help you manage massive amounts of data and provide timely access to mission-critical data for faster time to discovery.  For the end-to-end workflow we have designed a balanced HPC cluster that can be configured to include GPU capacity for required tasks but also improves the price/performance by keeping some of the tasks on the CPU.  Extreme requirements of Cryo-EM stress conventional storage and the extremely scalable Cray ClusterStor E1000 parallel filesystem speeds up the entire workflow, from data collection to rendering the final structure.

Get The Most Out of Limited Access to Cryo-EM Resources

Scarcity is the first challenge most structural biologists will face when trying to get time scheduled on a Cryo-EM microscope.  There are a limited number of scopes and “scope hours” available to individual researchers.  HPE’s Cryo-EM Pre-Processing System Blueprint provides the computing power and High Performance Storage needed to give researchers pre-processing results quickly, while experiments are still running.  This can help scientists identify issues and make adjustments during an experiment so that they can get the most out of limited Cryo-EM microscope time.

Reach Scientific Insights Faster

The second challenge investigators face is the challenge if discovery.  Scientific insight is an iterative process and having insufficient resources available may limit the iterations and approaches taken by a researcher on the search for scientific insight.  HPE’s Cryo-EM Image Analysis system blueprint couples the right combination of computing infrastructure with high performance storage to allow researchers to more quickly reconstruct molecular structures from Cryo-EM images…accelerating their overall scientific research process.

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