Cloud CPFP: A Shotgun Proteomics Data Analysis Pipeline Using Cloud and High Performance Computing

We have extended the functionality of the Central Proteomics
Facilities
Pipeline (CPFP) to allow use of remote cloud and high performance
computing (HPC) resources for shotgun proteomics data processing.
CPFP has been modified to include modular local and remote scheduling
for data processing jobs. The pipeline can now be run on a single
PC or server, a local cluster, a remote HPC cluster, and/or the Amazon
Web Services (AWS) cloud. We provide public images that allow easy
deployment of CPFP in its entirety in the AWS cloud. This significantly
reduces the effort necessary to use the software, and allows proteomics
laboratories to pay for compute time ad hoc, rather than obtaining
and maintaining expensive local server clusters. Alternatively the
Amazon cloud can be used to increase the throughput of a local installation
of CPFP as necessary. We demonstrate that cloud CPFP allows users
to process data at higher speed than local installations but with
similar cost and lower staff requirements. In addition to the computational
improvements, the web interface to CPFP is simplified, and other functionalities
are enhanced. The software is under active development at two leading
institutions and continues to be released under an open-source license
at http://cpfp.sourceforge.net.