scholarly journals Decision letter: Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud

2015 ◽  
Keyword(s):  
Electron Microscopy ◽  
Single Particle ◽  
High Performance ◽  
Low Cost ◽  
Cryo Electron Microscopy ◽  
Electron Microscopy Data ◽  
Microscopy Data

scholarly journals Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud

2015 ◽  
Author(s):  
Michael A. Cianfrocco ◽  
Andres E. Leschziner
Keyword(s):  
Electron Microscopy ◽  
Single Particle ◽  
High Performance ◽  
Low Cost ◽  
Cost Effective ◽  
Cryo Electron Microscopy ◽  
Software Packages ◽  
Electron Microscopes ◽  
Microscopy Data ◽  
New Generation

The advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high-resolution structures. However, calculating these structures requires high performance computing clusters, a resource that may be limiting to many likely cryo-EM users. To address this limitation and facilitate the spread of cryo-EM, we developed a publicly available ‘off-the-shelf’ computing environment on Amazon’s elastic cloud computing infrastructure. This environment provides users with single particle cryo-EM software packages and the ability to create computing clusters that can range in size from 16 to 480+ CPUs. Importantly, these computing clusters are also cost-effective, as we illustrate here by determining a near-atomic resolution structure of the 80S yeast ribosome for $28.89 USD in ~10 hours.

scholarly journals Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Michael A Cianfrocco ◽  
Andres E Leschziner
Keyword(s):  
Electron Microscopy ◽  
Cloud Computing ◽  
High Resolution ◽  
Single Particle ◽  
High Performance ◽  
Low Cost ◽  
Computing Environment ◽  
Cryo Electron Microscopy ◽  
Electron Microscopes ◽  
Microscopy Data

The advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high-resolution structures. Calculating these structures requires high performance computing clusters, a resource that may be limiting to many likely cryo-EM users. To address this limitation and facilitate the spread of cryo-EM, we developed a publicly available ‘off-the-shelf’ computing environment on Amazon's elastic cloud computing infrastructure. This environment provides users with single particle cryo-EM software packages and the ability to create computing clusters with 16–480+ CPUs. We tested our computing environment using a publicly available 80S yeast ribosome dataset and estimate that laboratories could determine high-resolution cryo-EM structures for $50 to $1500 per structure within a timeframe comparable to local clusters. Our analysis shows that Amazon's cloud computing environment may offer a viable computing environment for cryo-EM.

scholarly journals Towards on-the-fly Cryo-Electron Microscopy Data Processing by High Performance Data Analysis

2018 ◽  
Vol 955 ◽  
pp. 012005 ◽  
Author(s):  
Evgeny Pichkur ◽  
Timur Baimukhametov ◽  
Anton Teslyuk ◽  
Anton Orekhov ◽  
Roman Kamyshinsky ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Data Analysis ◽  
Data Processing ◽  
High Performance ◽  
Performance Data ◽  
Cryo Electron Microscopy ◽  
Electron Microscopy Data ◽  
Microscopy Data

scholarly journals Live Analysis and Reconstruction of Single-Particle Cryo-Electron Microscopy Data with CryoFLARE

2020 ◽  
Vol 60 (5) ◽  
pp. 2561-2569 ◽  
Author(s):  
Andreas D. Schenk ◽  
Simone Cavadini ◽  
Nicolas H. Thomä ◽  
Christel Genoud
Keyword(s):  
Electron Microscopy ◽  
Single Particle ◽  
Cryo Electron Microscopy ◽  
Electron Microscopy Data ◽  
Microscopy Data

CryoPoseNet: End-to-End Simultaneous Learning of Single-particle Orientation and 3D Map Reconstruction from Cryo-electron Microscopy Data

2021 ◽  
Author(s):  
Youssef S. G. Nashed ◽  
Frederic Poitevin ◽  
Harshit Gupta ◽  
Geoffrey Woollard ◽  
Michael Kagan ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Single Particle ◽  
Particle Orientation ◽  
Cryo Electron Microscopy ◽  
Electron Microscopy Data ◽  
End To End ◽  
Microscopy Data

scholarly journals Real-time cryo-electron microscopy data preprocessing with Warp

2019 ◽  
Vol 16 (11) ◽  
pp. 1146-1152 ◽  
Author(s):  
Dimitry Tegunov ◽  
Patrick Cramer
Keyword(s):  
Electron Microscopy ◽  
Real Time ◽  
Data Preprocessing ◽  
Cryo Electron Microscopy ◽  
Electron Microscopy Data ◽  
Microscopy Data

scholarly journals An improved method for phasing crystal structures with low non-crystallographic symmetry using cryo-electron microscopy data

2015 ◽  
Vol 6 (12) ◽  
pp. 919-923 ◽  
Author(s):  
Jia Wang ◽  
Weiguang Wang ◽  
Wen Song ◽  
Zhifu Han ◽  
Heqiao Zhang ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Crystal Structures ◽  
Improved Method ◽  
Cryo Electron Microscopy ◽  
Electron Microscopy Data ◽  
Crystallographic Symmetry ◽  
Microscopy Data
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