Federation in Genomics Pipelines: Techniques and Challenges
Somali Chaterji, Jinkyu Koo, Ninghui Li, Folker Meyer, Ananth Grama, and Saurabh Bagchi

Abstract
Federation is a popular concept in building distributed cyberinfrastructures, whereby computational
resources are provided by multiple organizations through a unified portal, decreasing the complexity of
moving data back and forth among multiple organizations. Federation has been used in bioinformatics
only to a limited extent, namely, federation of datastores, e.g., SBGrid Consortium for structural biology
and Gene Expression Omnibus (GEO) for functional genomics data. Here, we posit that it is important
to federate both computational resources (CPU, GPU, FPGA, etc.) and datastores to support popular
bioinformatics portals, that are faced with fast-increasing data volumes and increasing processing
requirements. A prime example, and one that we discuss here, is in genomics and metagenomics. Here,
it is critical that the processing of the data be done without having to transport the data across large
network distances. We exemplify our design and development through our experience with MG-RAST, the
most popular metagenomics portal and analysis pipeline. Currently, it is hosted completely at Argonne
National Laboratory (ANL). However, through a recently started National Institutes of Health (NIH) project
at Purdue University and ANL, we are taking steps toward federating this infrastructure. Being a widely
used resource, we have to move toward federation without disrupting the over 40K daily users. In this
paper, we describe the computational tools that will be useful for federating a bioinformatics infrastructure
and the open research challenges that we see in federating such infrastructures. Our manuscript can
hopefully serve to spur greater federation of bioinformatics infrastructures by showing the steps involved,
and thus, allow them to scale to support larger user bases.

Contact: Dr. Somali Chaterji; schaterji@purdue.edu

Supplementary information: Supplementary data are available at Briefings in Bioinformatics online.

Keywords: Computational genomics, cyberinfrastructure, federation, identity management, MG-RAST,
genomic privacy.