AstroTaverna—Building workflows with Virtual Observatory services

Ruíz, José Enrique; Garrido, Julián; Santander-Vela, J. D.; Sánchez–Expósito, S.; Verdes–Montenegro, L.

doi:10.1016/j.ascom.2014.09.002

Cited by 27 publications

(26 citation statements)

References 16 publications

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“…In the framework of Wf4Ever project, 15 the Astrophysics community has developed more than 50 workflows using Taverna 16 (Wolstencroft et al, 2013) and the AstroTaverna 17 plugin (Ruiz et al, 2014). AstroTaverna integrates existing Virtual Observatory web services as first-class building blocks in Taverna (e.g.…”

Section: Vo Oriented Workflowsmentioning

confidence: 99%

VO-compliant workflows and science gateways

Castelli

Taffoni

Sciacca

et al. 2015

Astronomy and Computing

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a b s t r a c tWorkflow and science gateway technologies have been adopted by scientific communities as a valuable tool to carry out complex experiments. They offer the possibility to perform computations for data analysis and simulations, whereas hiding details of the complex infrastructures underneath. There are many workflow management systems covering a large variety of generic services coordinating execution of workflows. In this paper we describe our experiences in creating workflows oriented science gateways based on gUSE/WS-PGRADE technology and in particular we discuss the efforts devoted to develop a VO-compliant web environment.

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Section: Vo Oriented Workflowsmentioning

confidence: 99%

VO-compliant workflows and science gateways

Castelli

Taffoni

Sciacca

et al. 2015

Astronomy and Computing

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“…In their work for AstroTaverna, Ruiz et al (2014) list the most important approaches for workflow management in astrophysics outside the scope of SGWs. Their conclusion is still valid, that those approaches solve very specific scientific cases with specialized data reduction.…”

Section: Workflow Composition In Astrophysicsmentioning

confidence: 99%

“…Those steps may not be easy to assemble, share and modify outside of a dedicated workflow manager. To overcome this problem, Ruiz et al (2014) propose AstroTaverna, which is a plugin for Taverna workflow manager that brings VO services.…”

Section: E-mail Address: Tlouge@irapompeu (T Louge)mentioning

confidence: 99%

CASAS: A tool for composing automatically and semantically astrophysical services

Louge

Karray

Archimède

et al. 2017

Astronomy and Computing

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“…For example, the myGrid project proposes Taverna [10][11], a scientific workflow management system (SWFMS) for composing automatic workflows emerged in bioinformatics. Nowadays, Taverna workbench has been widely deployed in a variety of research fields including biodiversity [12], chemistry, astronomy [13], data and text mining, digitization, document and image analysis, etc. Many Taverna distributions are open source and support for a variety of running environments including the Workbench, desktop client application, the Command Line Tool for a quick execution of workflows from a terminal, the Server for remote execution of workflows, the Player (a web interface plugin for submitting remote execution of workflows), and Taverna Online providing researchers to create Taverna workflows from a web browser.…”

Section: Tavernamentioning

confidence: 99%

Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services

Damkliang

Tandayya

Sangket

et al. 2016

Journal of Integrative Bioinformatics

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SummaryAt the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format. The workflow supports 1,000 to 20,000 numbers in bootstrapping replication. The workflow performs the tree inferring such as Parsimony (PARS), Distance Matrix -Neighbor Joining (DIST-NJ), and Maximum Likelihood (ML) algorithms of EMBOSS PHYLIPNEW package based on our proposed Multiple Sequence Alignment (MSA) similarity score. The local web services are implemented and deployed into two types using the Soaplab2 and Apache Axis2 deployment. There are SOAP and Java Web Service (JWS) providing WSDL endpoints to Taverna Workbench, a workflow manager. The workflow has been validated, the performance has been measured, and its results have been verified. Our workflow's execution time is less than ten minutes for inferring a tree with 10,000 replicates of the bootstrapping numbers. This paper proposes a new integrated automatic workflow which will be beneficial to the bioinformaticians with an intermediate level of knowledge and experiences. The all local services have been deployed at our portal http://bioservices.sci.psu.ac.th.

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AstroTaverna—Building workflows with Virtual Observatory services

Cited by 27 publications

References 16 publications

VO-compliant workflows and science gateways

VO-compliant workflows and science gateways

CASAS: A tool for composing automatically and semantically astrophysical services

Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services

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