title: Developing eThread pipeline using SAGA-pilot abstraction for large-scale structural bioinformatics.
abstract: While most of computational annotation approaches are sequence-based, threading methods are becoming increasingly attractive because of predicted structural information that could uncover the underlying function. However, threading tools are generally compute-intensive and the number of protein sequences from even small genomes such as prokaryotes is large typically containing many thousands, prohibiting their application as a genome-wide structural systems biology tool. To leverage its utility, we have developed a pipeline for eThread--a meta-threading protein structure modeling tool, that can use computational resources efficiently and effectively. We employ a pilot-based approach that supports seamless data and task-level parallelism and manages large variation in workload and computational requirements. Our scalable pipeline is deployed on Amazon EC2 and can efficiently select resources based upon task requirements. We present runtime analysis to characterize computational complexity of eThread and EC2 infrastructure. Based on results, we suggest a pathway to an optimized solution with respect to metrics such as time-to-solution or cost-to-solution. Our eThread pipeline can scale to support a large number of sequences and is expected to be a viable solution for genome-scale structural bioinformatics and structure-based annotation, particularly, amenable for small genomes such as prokaryotes. The developed pipeline is easily extensible to other types of distributed cyberinfrastructure.
authors.affiliation: RADICAL, ECE, Rutgers University, New Brunswick, NJ 08901, USA.
authors.forename: Anjani
authors.initials: A
authors.lastname: Ragothaman
authors.affiliation: Center for Computation and Technology, Louisiana State University, Baton Rouge, LA 70803, USA.
authors.forename: Sairam Chowdary
authors.identifier: 0000-0003-0990-3321
authors.initials: SC
authors.lastname: Boddu
authors.affiliation: Center for Computation and Technology, Louisiana State University, Baton Rouge, LA 70803, USA.
authors.forename: Nayong
authors.identifier: 0000-0003-3412-9956
authors.initials: N
authors.lastname: Kim
authors.affiliation: Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Feinstein
authors.affiliation: Center for Computation and Technology, Louisiana State University, Baton Rouge, LA 70803, USA ; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
authors.forename: Michal
authors.identifier: 0000-0002-6204-2869
authors.initials: M
authors.lastname: Brylinski
authors.affiliation: RADICAL, ECE, Rutgers University, New Brunswick, NJ 08901, USA.
authors.forename: Shantenu
authors.initials: S
authors.lastname: Jha
authors.affiliation: Center for Computation and Technology, Louisiana State University, Baton Rouge, LA 70803, USA.
authors.forename: Joohyun
authors.initials: J
authors.lastname: Kim
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D016678:Genome; D020407:Internet; D058977:Molecular Sequence Annotation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins