Marek Kasztelnik1, Ernesto Coto2, Marian Bubak3, Maciej Malawski4, Piotr Nowakowski5, Juan Arenas6, Alfredo Saglimbeni7, Debora Testi8, Alejandro F Frangi9. 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.
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.
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.
Authors: Luis Martí-Bonmatí; Ángel Alberich-Bayarri; Ruth Ladenstein; Ignacio Blanquer; J Damian Segrelles; Leonor Cerdá-Alberich; Polyxeni Gkontra; Barbara Hero; J M García-Aznar; Daniel Keim; Wolfgang Jentner; Karine Seymour; Ana Jiménez-Pastor; Ismael González-Valverde; Blanca Martínez de Las Heras; Samira Essiaf; Dawn Walker; Michel Rochette; Marian Bubak; Jordi Mestres; Marco Viceconti; Gracia Martí-Besa; Adela Cañete; Paul Richmond; Kenneth Y Wertheim; Tomasz Gubala; Marek Kasztelnik; Jan Meizner; Piotr Nowakowski; Salvador Gilpérez; Amelia Suárez; Mario Aznar; Giuliana Restante; Emanuele Neri Journal: Eur Radiol Exp Date: 2020-04-03