Auspice: Automatic Service Planning in Cloud/Grid Environments

Abstract

Scientific advancements have ushered in staggering amounts of available data and processes which are now scattered across various locations in the Web, Grid, and more recently, the Cloud. These processes and data sets are often semantically loosely-coupled and must be composed together piecemeal to generate scientific workflows. Understanding how to design, manage, and execute such data-intensive workflows has become increasingly esoteric, confined to a few scientific experts in the field. Despite the development of scientific workflow management systems, which have simplified workflow planning to some extent, a means to reduce the complexity of user interaction without forfeiting some robustness has been elusive. This violates the essence of scientific progress, where information should be accessible to anyone.A high-level querying interface tantamount to common search engines that can not only return a relevant set of scientific workflows, but also facilitate their execution, may be highly beneficial to users.The development of such a system that can abstract the complex task of scientific workflow planning and execution from the user is reported herein. Our system, Auspice: AUtomatic Service Planning In Cloud/Grid Environments, consists of the following key contributions. Initially, a two-level metadata management framework is introduced. In the top-level, Auspice captures semantic dependencies among available, shared processes and data sets with an ontology. Our system furthermore indexes these shared resources for facilitating fast planning times. This metadata ii To my family, friends, and mentors. iv ACKNOWLEDGMENTS This work is far from complete without proper acknowledgment of those who supported me over the years. My family. When my parents made the decision to move to Ohio from Taiwan over twenty years ago, it was not the ideal situation for either of them. My mother spent tireless hours teaching me English and we struggled through heaps of schoolwork together. My father kept the family afloat through his ongoing work overseas. He also brought me up with great values in life, including humility and patience. Without their sacrifice and guidance, my education would have been impossible. I also thank my sister, Jenn, who has always been my partner in crime in childhood and now.My wife, Michelle, for her infinite patience and unwavering love and understanding during even the most trying times. I am thankful for the many drop-offs and pick-ups to/from Dreese Labs she has had to perform on early mornings and late evenings. I respect her deeply, and she is a great inspiration to me.

Development of a Dissemination Platform for Spatiotemporal and Phylogenetic Analysis of Avian Infectious Bronchitis Virus

“…To visualize the evolution and spread of IBV in an interactive tool that allows for near real-time updates using phylogenetic, spatial, and epidemic information based on outbreak data ( Supplementary Table 5 ), we used Nextstrain ( https://nextstrain.org ) ( 40 ). IBV sequences were processed in Nextstrain's platform using the Augur bioinformatics toolkit (augur) ( 67 ) and visualized using Auspice ( https://github.com/nextstrain/auspice ) ( 68 ). Auspice is designed to provide a detailed view of the results of the Augur analysis.…”

“…IBV sequences were processed in Nextstrain's platform using the Augur bioinformatics toolkit (augur) (67) and visualized using Auspice (https://github. com/nextstrain/auspice) (68). Auspice is designed to provide a detailed view of the results of the Augur analysis.…”