Low cost, high performance processing of single particle cryo-EM data in the cloud 


Michael A. Cianfrocco & Andres E. Leschziner (2015) 




                                                                     
                    Getting Started    
Running a job on a single machine   
Data storage  
Setting up & running a cluster on Amazon EC2
                                               
   
   
                                            
                                       relion2
https://groups.google.com/forum/#!forum/cryo-em-in-the-cloud     
Tutorial
                                                                          


Latest updates:

February 28, 2017

We have developed new tools for AWS and Relion, and we have incorporated them into a NEW website. You can find it here: 


This means that while we will leave this website up, you can find up-to-date information on our new site. 

January 1, 2017

We wrote software tools to help launch & stop instances from the command line, with minimal user acrobatics. Check how to set it up and use it on Github: https://github.com/leschzinerlab/AWS


October 8, 2016

Performed benchmarking tests on p2 GPU instances using Relion's benchmarking test case. Read more here.


October 4, 2016

We have installed Relion-2.0beta along (with all required software) to do cryo-EM data processing on the p2 virtual machines on AWS. Read more here


September 21, 2015

We created documentation describing how to upload your data onto Amazon S3, and also detailed the differences between EBS volumes and S3 buckets. This can be found within the Data Storage web page (Link).


September 18, 2015

You can now find information about copying files onto and off-of a STARcluster (by request from users). (Link


June 12, 2015 

IMPORTANT ANNOUNCEMENT - STARcluster doesn't work in EU-Central-1. Based upon feedback from users (thanks Hugo Munoz Hernandez!), I discovered a problem with the STARcluster software that I copied to EU-Central-1. This will be resolved in the coming days, you'll see an announcement here when the problem is fixed.


May 8, 2015

Our paper on using Amazon's cloud for cryo-EM image analysis is published! eLife article in press!


April 22, 2015

New release! EM-packages-in-the-Cloud-v3.93 and EM-packages-in-the-Cloud-Node-v3.1! 

Not a huge upgrade, but a few things: 

EM-packages-in-the-Cloud-Node-v3.1:

-EMAN1.9 was added to the available software 

EM-packages-in-the-Cloud-v3.93:

-STARcluster config file was updated to include FORCE_SPOT_MASTER=True so that, by default, the STARcluster master node is booted up as a spot instance. Users won't have to specify this over the command line.

-The AMI for the latest EM-Packages-in-the-Cloud-Node-v3.1 was included within the STARcluster config file

-Removed STARcluster 'mykey' so that new users don't have to remove 'mykey' when creating a STARcluster key.

These new AMIs have been updated globally & are publicly available.


March 18, 2015

The preprint of our manuscript is now online at bioArxiv! Check it out here


March 10, 2015

To improve the day-to-day workflow of using Amazon's EC2, we added step-by-step instructions to install STARcluster locally on your personal PC. This allows users to launch a single instance or a cluster without having to open up the AWS console. You can find more info here.


March 5, 2015

We've added a detailed discussion of security considerations that all AWS users should take advantage of within the Getting Started section.  


February 27, 2015

EM-packages-in-the-Cloud-3.92 and EM-packages-in-the-Cloud-v3.0-Node are now copied to all regions across the globe: 

US East (N. Virginia)
US West (Oregon)
US West (N. California)
EU (Ireland)
EU (Frankfurt)
Asia Pacific (Singapore)
Asia Pacific (Tokyo)
Asia Pacific (Sydney)
South America (São Paulo)


January 27, 2015

EM-packages-in-the-Cloud-3.92 released! More software programs were added to the environment, so that the current list of software programs are: 

Relion-1.3
EMAN2-2.1
Sparx
EMAN1-1.9
Frealign-9.08
Xmipp-2.4
ctffind3 & ctftilt
Signature
Spider-22.03
TiltPicker

January 8, 2015

Website has been updated with a new layout and more specific help on how to store data on EBS volumes.