Support for Taverna workflows in the VPH-Share cloud platform

Marek Kasztelnik; Ernesto Coto; Marian Bubak; Maciej Malawski; Piotr Nowakowski; Juan Arenas; Alfredo Saglimbeni; Debora Testi; Alejandro F Frangi

doi:10.1016/j.cmpb.2017.05.006

Support for Taverna workflows in the VPH-Share cloud platform

Comput Methods Programs Biomed. 2017 Jul:146:37-46. doi: 10.1016/j.cmpb.2017.05.006. Epub 2017 May 20.

Authors

Marek Kasztelnik¹, Ernesto Coto², Marian Bubak³, Maciej Malawski⁴, Piotr Nowakowski⁵, Juan Arenas⁶, Alfredo Saglimbeni⁷, Debora Testi⁸, Alejandro F Frangi⁹

Affiliations

¹ ACC Cyfronet AGH, Krakow, Poland. Electronic address: m.kasztelnik@cyfronet.pl.
² Centre for Computational Imaging & Simulation Technologies in Biomedicine (CISTIB), Electronic and Electrical Engineering Department, The University of Sheffield, Sheffield, UK. Electronic address: e.coto@sheffield.ac.uk.
³ ACC Cyfronet AGH, Krakow, Poland; Department of Computer Science, AGH University of Science and Technology, Krakow, Poland. Electronic address: bubak@agh.edu.pl.
⁴ ACC Cyfronet AGH, Krakow, Poland; Department of Computer Science, AGH University of Science and Technology, Krakow, Poland. Electronic address: malawski@agh.edu.pl.
⁵ ACC Cyfronet AGH, Krakow, Poland. Electronic address: p.nowakowski@cyfronet.pl.
⁶ Centre for Computational Imaging & Simulation Technologies in Biomedicine (CISTIB), Electronic and Electrical Engineering Department, The University of Sheffield, Sheffield, UK. Electronic address: j.arenas@sheffield.ac.uk.
⁷ CINECA SuperComputing Centre, Casalecchio di Reno, Italy. Electronic address: a.saglimbeni@scsitaly.com.
⁸ CINECA SuperComputing Centre, Casalecchio di Reno, Italy. Electronic address: d.testi@cineca.it.
⁹ Centre for Computational Imaging & Simulation Technologies in Biomedicine (CISTIB), Electronic and Electrical Engineering Department, The University of Sheffield, Sheffield, UK. Electronic address: a.frangi@sheffield.ac.uk.

PMID: 28688488
DOI: 10.1016/j.cmpb.2017.05.006

Abstract

Background and objective: To address the increasing need for collaborative endeavours within the Virtual Physiological Human (VPH) community, the VPH-Share collaborative cloud platform allows researchers to expose and share sequences of complex biomedical processing tasks in the form of computational workflows. The Taverna Workflow System is a very popular tool for orchestrating complex biomedical & bioinformatics processing tasks in the VPH community. This paper describes the VPH-Share components that support the building and execution of Taverna workflows, and explains how they interact with other VPH-Share components to improve the capabilities of the VPH-Share platform.

Methods: Taverna workflow support is delivered by the Atmosphere cloud management platform and the VPH-Share Taverna plugin. These components are explained in detail, along with the two main procedures that were developed to enable this seamless integration: workflow composition and execution.

Results: 1) Seamless integration of VPH-Share with other components and systems. 2) Extended range of different tools for workflows. 3) Successful integration of scientific workflows from other VPH projects. 4) Execution speed improvement for medical applications.

Conclusion: The presented workflow integration provides VPH-Share users with a wide range of different possibilities to compose and execute workflows, such as desktop or online composition, online batch execution, multithreading, remote execution, etc. The specific advantages of each supported tool are presented, as are the roles of Atmosphere and the VPH-Share plugin within the VPH-Share project. The combination of the VPH-Share plugin and Atmosphere engenders the VPH-Share infrastructure with far more flexible, powerful and usable capabilities for the VPH-Share community. As both components can continue to evolve and improve independently, we acknowledge that further improvements are still to be developed and will be described.

Keywords: Atmosphere cloud; RESTful API; Taverna workflow; VPH-Share.

MeSH terms

Cloud Computing*
Computational Biology*
Software
Workflow*