Experience using web services for biological sequence analysis

Stockinger, Heinz; Attwood, Teresa K.; Chohan, Shahid Nadeem; Côté, Richard G.; Cudré-Mauroux, Philippe; Falquet, Laurent; Fernandes, Pedro; Finn, Robert D.; Hupponen, Taavi; Korpelainen, Eija; Labarga, Alberto; Laugraud, Aurélie; Lima, Tânia; Pafilis, Evangelos; Pagni, Marco; Pettifer, Steve; Phan, Isabelle; Rahman, Nazim

doi:10.1093/bib/bbn029

Cited by 25 publications

(23 citation statements)

References 26 publications

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“…In this respect REST is better suited for explorative development, and SOAP for building large, long-lasting software infrastructure. Applicability of both technologies to bioinformatics is further discussed in [16].…”

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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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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“…Perl or Python) and protocols (SOAP or REST) at http://www.ebi.ac.uk/Tools/webservices/ tutorials/06_programming. For background information on web services in bioinformatics, we refer to reader to [14,15]. The tool specific WSDL file is used by the user to produce the SOAP client, which sends a request to the remote SOAP server.…”

Section: Using the Ibivu Servicesmentioning

confidence: 99%

Protein analysis tools and services at IBIVU

Brandt¹,

Heringa

2011

Journal of Integrative Bioinformatics

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“…The registry thus acts as a web2.0 style community server, putting users and providers in touch with one another. [7] The approach of this project, embodied in its registry, is to recommend a set of industry-standard technologies defined by the Web Service Interoperability organization and to provide tools that help developers move towards adopting these, while at the same time recognizing that a wide variety of other approaches exist for pragmatic or historical reasons. The registry therefore allows all manner of services to be added, and aims to provide documentation and support for users wishing to bring their services in line with standard practices.…”

Section: Introductionmentioning

confidence: 99%

BioFactory: Semantic Integration of Biomedical Data and Applications

Wang

Hecht

Sheu

et al. 2012

2012 IEEE First International Conference on Internet Operating Systems

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Web services have become increasingly important in biomedical research as tools that allow databases and algorithms to be accessed programmatically as computational components in programs. Various biomedical web services differ in their definitions and invocation protocols, as well as their communication and data formats and this presents a barrier to biomedical web service interoperability and integration. In this study, we present Biofactory, a web portal that collects and integrates biomedical web services. Users are able to register/search by semantic computation. The semantic computing and Semantic Description language (SDL) seems ideally suited to help streamline the collection of different biomedical services by providing a common language and a generic format for problem formalization

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Experience using web services for biological sequence analysis

Cited by 25 publications

References 26 publications

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

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

Protein analysis tools and services at IBIVU

BioFactory: Semantic Integration of Biomedical Data and Applications

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