Sedna: A BPEL-Based Environment for Visual Scientific Workflow Modeling

Wassermann, Bruno; Emmerich, Wolfgang; Butchart, Ben; Cameron, Nick; Chen, Liang; Patel, Jignesh M.

doi:10.1007/978-1-84628-757-2_26

Cited by 53 publications

(32 citation statements)

References 202 publications

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“…OMII-BPEL (Open Middleware Infrastructure Institute BPEL [19]) aims to support the orchestration of scientific workflows with a multitude of service processes and longduration process executions. It provides a customised BPEL engine, and supports a set of constructs desirable for specification of scientific workflows.…”

Section: Implementing Composed Servicesmentioning

confidence: 99%

Formal Methods for Industrial Critical Systems

Alpuente¹,

Cook²,

Joubert³

2009

Lecture Notes in Computer Science

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Abstract.Creating new services through composition of existing ones is an attractive option. However, composition can be complex and service compatibility needs to be checked. A rigorous and industrially-usable methodology is therefore desirable required for creating, verifying, implementing and validating composed services. An explanation is given of the approach taken by CRESS (Communication Representation Employing Systematic Specification). Formal verification and validation are performed through automated translation to LOTOS (Language Of Temporal Ordering Specification). Implementation and validation are performed through automated translation to BPEL (Business Process Execution Logic) and WSDL (Web Services Description Language). The approach is illustrated with an application to grid service composition in e-Social Science.

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Section: Implementing Composed Servicesmentioning

confidence: 99%

Formal Methods for Industrial Critical Systems

Alpuente¹,

Cook²,

Joubert³

2009

Lecture Notes in Computer Science

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“…Efficient XML Interchange Format (EXI) 7 compacts XML documents using the XML Schema 8 to guide and optimize the process, resulting in better compression than gzip 9 . EXI documents are also faster in parsing and support streaming, which will definitely have impact on performance of SOAP Web Services in the future.…”

Section: Related Workmentioning

confidence: 99%

Data partitioning enables the use of standard SOAP Web Services in genome-scale workflows

Sztromwasser

Petersen

Puntervoll

2011

Journal of Integrative Bioinformatics

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SummaryBiological databases and computational biology tools are provided by research groups around the world, and made accessible on the Web. Combining these resources is a common practice in bioinformatics, but integration of heterogeneous and often distributed tools and datasets can be challenging. To date, this challenge has been commonly addressed in a pragmatic way, by tedious and error-prone scripting. Recently however a more reliable technique has been identified and proposed as the platform that would tie together bioinformatics resources, namely Web Services. In the last decade the Web Services have spread wide in bioinformatics, and earned the title of recommended technology. However, in the era of high-throughput experimentation, a major concern regarding Web Services is their ability to handle large-scale data traffic. We propose a stream-like communication pattern for standard SOAP Web Services, that enables efficient flow of large data traffic between a workflow orchestrator and Web Services. We evaluated the data-partitioning strategy by comparing it with typical communication patterns on an example pipeline for genomic sequence annotation. The results show that data-partitioning lowers resource demands of services and increases their throughput, which in consequence allows to execute in-silico experiments on genome-scale, using standard SOAP Web Services and workflows. As a proof-of-principle we annotated an RNA-seq dataset using a plain BPEL workflow engine.

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“…2007). Despite its textual nature, mostly research specify workflows in graphical notations and many tools exist to translate graphical workflow representations into BPEL script such as XBaya (Shirasuna 2011), OMII-BPEL (OMII-BPEL 2011), Sedna (Wassermann et al, 2007), etc. However, according to some workflow domain experts e.g.…”

Section: Background and Related Workmentioning

confidence: 99%