ABI Development: bioKepler: A Comprehensive Bioinformatics Scientific Workflow Module for Distributed Analysis of Large-Scale Biological Data

University Of California-San Diego, La Jolla CA

Investigators

Abstract

The University of California at San Diego is awarded a grant to create a Kepler Scientific Workflow System (http://kepler-project.org) module that facilitates the development of Kepler workflows for integrated execution of bioinformatics applications in distributed environments. Next-generation DNA sequencing generates a very large amount of sequence data that can be used in numerous applications addressing many scientific challenges. This places unprecedented demands on traditional single-processor bioinformatics algorithms. In addition, enabling bioinformaticians and computational biologists to conduct efficient analysis requires higher-level abstractions on top of scientific workflow systems and distributed computing methods. To develop such an environment, the bioKepler project will create scientific workflow components to execute a set of bioinformatics tools using distributed execution patterns. Once customized, these scientific workflow components will be executed on multiple distributed platforms including various Cloud and Grid computing platforms. The initial set of bioinformatics tools will be selected based on an evaluation and integration of a wide range of community tools and workflows to meet the diverse needs of researchers, organized into eight groups covering most aspect of bioinformatics applications: 1) Sequence database searches; 2) Mapping; 3) Sequence assembly; 4) Gene prediction; 5) Clustering; 6) Multiple sequence alignment, phylogeny and taxonomy; 7) Protein annotation; 8) Other miscellaneous utilities including data format transformation and parsing. The project will also study how these distributed execution patterns will affect or improve workflow scheduling and execution in distributed environments. In addition, the project will deliver virtual machines that include a Kepler engine and all the bioKepler components for bioinformatics tools and applications. The developed tools will be applicable to a wide range of bioinformatics and computational biology problems. The central rationale for the planned education and outreach efforts is the importance of training next generation scientists. This rationale also aligns with the primary goal of the project to provide tools to further bridge the gap between bioinformatics and technology. The impact of such an approach is multifold, including facilitating bioinformaticians (and potentially scientists from other disciplines) to conduct efficient, comprehensive and parallelized analyses using domain-specific distributed execution components without writing a single line of code. In addition to the project workshops, usage scenarios will be solicited via surveys with follow-up phone discussions, and representation at major domain conferences will solicit input on priorities and raise awareness of the products in later years. The bioKepler team is committed to diversity as demonstrated by the involvement of three females (including PI Altintas) in the group of seven funded personnel and the broad range of efforts to include underrepresented students. All the resource, materials and the open-source software products produced by the bioKepler ABI Development project will be integrated with the CAMERA (http://camera.calit2.net/) project for a community of nearly 4000 devoted users in over 75 countries worldwide, and will be made publicly available to a larger audience through the Kepler project website (http://kepler-project.org).