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

Cianfrocco MA, Leschziner AE - Elife (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus

Cryo-EM structure of 80S ribosome at an overall resolution of 4.6 Å.(A) Overall view of 80S reconstruction filtered to 4.6 Å while applying a negative B-factor of −116 Å2. (B) Gold standard FSC curve. (C) Selected regions from the 60S subunit. Cryo-EM maps were visualized with UCSF Chimera (Pettersen et al., 2004). Source data: Dryad Digital Repository dataset (http://datadryad.org/review?doi=doi:10.5061/dryad.9mb54) (Cianfrocco and Leschziner).DOI:http://dx.doi.org/10.7554/eLife.06664.007
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fig3: Cryo-EM structure of 80S ribosome at an overall resolution of 4.6 Å.(A) Overall view of 80S reconstruction filtered to 4.6 Å while applying a negative B-factor of −116 Å2. (B) Gold standard FSC curve. (C) Selected regions from the 60S subunit. Cryo-EM maps were visualized with UCSF Chimera (Pettersen et al., 2004). Source data: Dryad Digital Repository dataset (http://datadryad.org/review?doi=doi:10.5061/dryad.9mb54) (Cianfrocco and Leschziner).DOI:http://dx.doi.org/10.7554/eLife.06664.007

Mentions: To test the performance of Amazon's EC2 environment, we analyzed a previously published 80S Saccharomyces cerevisiae ribosome dataset (Bai et al., 2013) (EMPIAR 10002) on a 128 CPU cluster (8 × 16 CPUs; using the r3.8xlarge instance). After extracting 62,022 particles, we performed 2D classification within Relion. Subsequent 3D classification of the particles into four classes revealed that two classes adopted a similar structural state. We merged those two classes and used the associated particles to carry out a 3D refinement in Relion—we were able to obtain a structure with an overall resolution of 4.6 Å (Figure 3A–C).10.7554/eLife.06664.007Figure 3.Cryo-EM structure of 80S ribosome at an overall resolution of 4.6 Å.


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

Cianfrocco MA, Leschziner AE - Elife (2015)

Cryo-EM structure of 80S ribosome at an overall resolution of 4.6 Å.(A) Overall view of 80S reconstruction filtered to 4.6 Å while applying a negative B-factor of −116 Å2. (B) Gold standard FSC curve. (C) Selected regions from the 60S subunit. Cryo-EM maps were visualized with UCSF Chimera (Pettersen et al., 2004). Source data: Dryad Digital Repository dataset (http://datadryad.org/review?doi=doi:10.5061/dryad.9mb54) (Cianfrocco and Leschziner).DOI:http://dx.doi.org/10.7554/eLife.06664.007
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4440898&req=5

fig3: Cryo-EM structure of 80S ribosome at an overall resolution of 4.6 Å.(A) Overall view of 80S reconstruction filtered to 4.6 Å while applying a negative B-factor of −116 Å2. (B) Gold standard FSC curve. (C) Selected regions from the 60S subunit. Cryo-EM maps were visualized with UCSF Chimera (Pettersen et al., 2004). Source data: Dryad Digital Repository dataset (http://datadryad.org/review?doi=doi:10.5061/dryad.9mb54) (Cianfrocco and Leschziner).DOI:http://dx.doi.org/10.7554/eLife.06664.007
Mentions: To test the performance of Amazon's EC2 environment, we analyzed a previously published 80S Saccharomyces cerevisiae ribosome dataset (Bai et al., 2013) (EMPIAR 10002) on a 128 CPU cluster (8 × 16 CPUs; using the r3.8xlarge instance). After extracting 62,022 particles, we performed 2D classification within Relion. Subsequent 3D classification of the particles into four classes revealed that two classes adopted a similar structural state. We merged those two classes and used the associated particles to carry out a 3D refinement in Relion—we were able to obtain a structure with an overall resolution of 4.6 Å (Figure 3A–C).10.7554/eLife.06664.007Figure 3.Cryo-EM structure of 80S ribosome at an overall resolution of 4.6 Å.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus