ViPDAC uses Amazon Web Services to analyze proteomics data.
To use ViPDAC you first sign up for access to Amazon’s Web Services, then you can log in to the Amazon console which is used to start up a personal copy of the ViPDAC server. This starts ViPDAC running on one of Amazon’s servers from where you can now access the ViPDAC web interface. At this point normal proteomics analysis procedures take over - you can pick an existing set of parameters or configure a new analysis (cleavage enzyme, modifications, protein database to search, etc) and select your data file (spectra in .mgf format) and then submit the job. ViPDAC will then upload the data file to the your area on Amazon’s S3 storage and run the analysis using the EC2 nodes available in your cluster. Once the analysis is complete ViPDAC will compile the results and save them back onto S3 where they can be stored or downloaded to the desktop for further analysis. At this point you can continue to do more analyses or simply turn the cluster off until you need it again.
One of the benefits of the dynamic nature of the cloud is that if you want the analysis to go faster you can add more nodes to your cluster at any time.
ViPDAC Tutorial (PDF)
Brian D. Halligan - USHUPO 2009
Available Amazon Machine Images (AMI)