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

Marek Kasztelnik, Ernesto Coto, Marian Bubak, Maciej Malawski^*, Piotr Nowakowski, Juan Arenas, Alfredo Saglimbeni, Debora Testi, Alejandro F. Frangi

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	37-46
Number of pages	10
Journal	Computer Methods and Programs in Biomedicine
Volume	146
DOIs	https://doi.org/10.1016/j.cmpb.2017.05.006
Publication status	Published - Jul 2017

Keywords

Atmosphere cloud
RESTful API
Taverna workflow
VPH-Share

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10.1016/j.cmpb.2017.05.006

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@article{ab7db4c850124740901a65ed864c8f0d,

title = "Support for Taverna workflows in the VPH-Share cloud platform",

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",

author = "Marek Kasztelnik and Ernesto Coto and Marian Bubak and Maciej Malawski and Piotr Nowakowski and Juan Arenas and Alfredo Saglimbeni and Debora Testi and Frangi, {Alejandro F.}",

note = "Publisher Copyright: {\textcopyright} 2017 Elsevier B.V.",

year = "2017",

month = jul,

doi = "10.1016/j.cmpb.2017.05.006",

language = "English",

volume = "146",

pages = "37--46",

journal = "Computer Methods and Programs in Biomedicine",

issn = "0169-2607",

publisher = "Elsevier BV",

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T1 - Support for Taverna workflows in the VPH-Share cloud platform

AU - Kasztelnik, Marek

AU - Coto, Ernesto

AU - Bubak, Marian

AU - Malawski, Maciej

AU - Nowakowski, Piotr

AU - Arenas, Juan

AU - Saglimbeni, Alfredo

AU - Testi, Debora

AU - Frangi, Alejandro F.

PY - 2017/7

Y1 - 2017/7

N2 - 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.

AB - 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.

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KW - RESTful API

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SN - 0169-2607

VL - 146

SP - 37

EP - 46

JO - Computer Methods and Programs in Biomedicine

JF - Computer Methods and Programs in Biomedicine

ER -

Support for Taverna workflows in the VPH-Share cloud platform

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Keywords

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