Yabi: An online research environment for grid, high performance and cloud computing.

Source Code for Biology and Medicine
Adam A HunterMatthew I Bellgard

Abstract

There is a significant demand for creating pipelines or workflows in the life science discipline that chain a number of discrete compute and data intensive analysis tasks into sophisticated analysis procedures. This need has led to the development of general as well as domain-specific workflow environments that are either complex desktop applications or Internet-based applications. Complexities can arise when configuring these applications in heterogeneous compute and storage environments if the execution and data access models are not designed appropriately. These complexities manifest themselves through limited access to available HPC resources, significant overhead required to configure tools and inability for users to simply manage files across heterogenous HPC storage infrastructure. In this paper, we describe the architecture of a software system that is adaptable to a range of both pluggable execution and data backends in an open source implementation called Yabi. Enabling seamless and transparent access to heterogenous HPC environments at its core, Yabi then provides an analysis workflow environment that can create and reuse workflows as well as manage large amounts of both raw and processed data in a secure and flexibl...Continue Reading

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Citations

Apr 2, 2013·Briefings in Bioinformatics·Nathan S Watson-HaighMaria V Schneider
Sep 7, 2013·Genome Announcements·Paula M MoolhuijzenDonald M Gardiner
Oct 18, 2013·Source Code for Biology and Medicine·Matthew BellgardAdam Hunter
Dec 18, 2013·Investigative Genetics·Megan L CoghlanMichael Bunce
Jul 2, 2014·Source Code for Biology and Medicine·Matthew I BellgardAdam Hunter
Jun 14, 2013·Journal of Chemical Information and Modeling·W Patrick Walters
Dec 17, 2015·Mass Spectrometry Reviews·Gerben Menschaert, David Fenyö
Aug 12, 2014·Journal of Paediatrics and Child Health·Gareth BaynamJack Goldblatt
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Nov 28, 2019·PeerJ·Markus Joppich, Ralf Zimmer
Oct 14, 2017·Archives of Virology·Arnaud G BlouinRobin M MacDiarmid
Dec 13, 2018·Journal of Chemical Information and Modeling·Thomas KainradThierry Langer

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Software Mentioned

TPP
GridFTP
SSH
Trans
Yabish
Ajax
Yabi Resource Manager
Crispin
Python
Biojava

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