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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

Availability of virtual machines within regions at specified spot instance prices.For each Amazon region (excluding SA-East-1, which does not offer r3.8xlarge instances), r3.8xlarge spot instance prices were retrieved for each availability zone, where separate availability zones are shown as separate data points for a given spot instance price. (Note: each region can have different number of availability zones). From the spot instance prices, the percentage time of the spot instances that were spent below the specified spot instance price were calculated. The average value is shown as a solid black line. Source data: Figure 2—source data 1.DOI:http://dx.doi.org/10.7554/eLife.06664.006
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fig2s1: Availability of virtual machines within regions at specified spot instance prices.For each Amazon region (excluding SA-East-1, which does not offer r3.8xlarge instances), r3.8xlarge spot instance prices were retrieved for each availability zone, where separate availability zones are shown as separate data points for a given spot instance price. (Note: each region can have different number of availability zones). From the spot instance prices, the percentage time of the spot instances that were spent below the specified spot instance price were calculated. The average value is shown as a solid black line. Source data: Figure 2—source data 1.DOI:http://dx.doi.org/10.7554/eLife.06664.006

Mentions: In order to determine if spot instances offer a consistent reduction in price, we analyzed the global availability of r3.8xlarge spot instances. Currently, Amazon has 9 regions worldwide within 7 countries: US-East-1 (United States), US-West-1 (United States), US-West-2 (United States), SA-East-1 (Brazil), EU-Central-1 (Germany), EU-West-1 (Ireland), AP-Northeast-1 (Japan), AP-Southeast-1 (Singapore), and AP-Southeast-2 (Australia). For each region, we retrieved spot instance prices for r3.8xlarge instances over the past 3 months and analyzed the time they spent at prices below $0.35–$0.65/hr (corresponding to discounts of 87.5–76.8% over the full on-demand rate of $2.80/hr) (Figure 2 and Figure 2—figure supplement 1). This analysis revealed that, globally, 49.8% of r3.8xlarge instances were below $0.35/hr, 12.5% the on-demand price (Figure 2). For $0.65/hr, 76.5% below full price, one could access 82.2% of the global r3.8xlarge spot instances. These data indicate that spot instances provide dependable, cost-effective access to Amazon's computing resources.10.7554/eLife.06664.004Figure 2.Global availability of Amazon r3.8xlarge spot instances.


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

Cianfrocco MA, Leschziner AE - Elife (2015)

Availability of virtual machines within regions at specified spot instance prices.For each Amazon region (excluding SA-East-1, which does not offer r3.8xlarge instances), r3.8xlarge spot instance prices were retrieved for each availability zone, where separate availability zones are shown as separate data points for a given spot instance price. (Note: each region can have different number of availability zones). From the spot instance prices, the percentage time of the spot instances that were spent below the specified spot instance price were calculated. The average value is shown as a solid black line. Source data: Figure 2—source data 1.DOI:http://dx.doi.org/10.7554/eLife.06664.006
© Copyright Policy
Related In: Results  -  Collection

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

fig2s1: Availability of virtual machines within regions at specified spot instance prices.For each Amazon region (excluding SA-East-1, which does not offer r3.8xlarge instances), r3.8xlarge spot instance prices were retrieved for each availability zone, where separate availability zones are shown as separate data points for a given spot instance price. (Note: each region can have different number of availability zones). From the spot instance prices, the percentage time of the spot instances that were spent below the specified spot instance price were calculated. The average value is shown as a solid black line. Source data: Figure 2—source data 1.DOI:http://dx.doi.org/10.7554/eLife.06664.006
Mentions: In order to determine if spot instances offer a consistent reduction in price, we analyzed the global availability of r3.8xlarge spot instances. Currently, Amazon has 9 regions worldwide within 7 countries: US-East-1 (United States), US-West-1 (United States), US-West-2 (United States), SA-East-1 (Brazil), EU-Central-1 (Germany), EU-West-1 (Ireland), AP-Northeast-1 (Japan), AP-Southeast-1 (Singapore), and AP-Southeast-2 (Australia). For each region, we retrieved spot instance prices for r3.8xlarge instances over the past 3 months and analyzed the time they spent at prices below $0.35–$0.65/hr (corresponding to discounts of 87.5–76.8% over the full on-demand rate of $2.80/hr) (Figure 2 and Figure 2—figure supplement 1). This analysis revealed that, globally, 49.8% of r3.8xlarge instances were below $0.35/hr, 12.5% the on-demand price (Figure 2). For $0.65/hr, 76.5% below full price, one could access 82.2% of the global r3.8xlarge spot instances. These data indicate that spot instances provide dependable, cost-effective access to Amazon's computing resources.10.7554/eLife.06664.004Figure 2.Global availability of Amazon r3.8xlarge spot instances.

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