Exploring Williams–Beuren syndrome using myGrid

Stevens, Robert; Tipney, Hannah; Wroe, Chris; Oinn, Tom; Senger, Martin; Lord, Phillip; Goble, Carole; Brass, Andy; Tassabehji, May

doi:10.1093/bioinformatics/bth944

Cited by 85 publications

(55 citation statements)

References 16 publications

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“…When we started out, we replicated current scientific practice. The focus was on interoperating services, making services accessible and workflow creation [6]. Two years later we were inventing new practice: workflows had to integrate data not just link services; discovery had become an issue with so many services; and workflow editing and reuse was as important as creation from scratch.…”

Section: Know Your Usersmentioning

confidence: 99%

Software Design for Empowering Scientists

Roure

Goble

2009

IEEE Softw.

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Scientific research is increasingly digital. Some activities, like data analysis, search and simulation, can be accelerated by enabling scientists to write workflows and scripts that automate routine activities. These capture pieces of scientific method that can be shared with others. The Taverna Workbench, a widely deployed scientific workflow management system, together with the myExperiment social web site for the sharing of scientific experiments, have been devised according to six principles of designing software for adoption by scientists and six principles of user engagement.Science is becoming increasingly digital, and the scientist's tools are not just the experimental apparatus of the laboratory but also the software apparatus which they use to conduct their researchto analyse data, to search databases, to run simulations and to record their scientific process. New experimental methods -from DNA microarrays to sensor networks in the environment -are generating volumes of data that, without software assistance, just wouldn't get processed.Watch a researcher at work and we see lots of activity at the computer, using applications, services and data that might be local to the laboratory, the enterprise, or out on the Web. These new research tools and methods are evident across a very broad spectrum of disciplines. Some, like bioinformaticians working with protein sequences, might conduct some of their research entirely in silico. Meanwhile, chemists in the laboratory are looking up procedures, designing their experiments, conducting and recording their work, and running simulations, searches and analyses. Climate change researchers are capturing the latest data from radar images and sensor networks, and running and testing their models. Musicologists are extracting features from recorded music as part of musical analysis. Archaeologists are exploring 3D visualisations of their digs.Some of the processing is highly repetitive -repeating processes with new data, varying parameters, and making small changes to the process. It clearly helps speed things up and makes them more repeatable if some of this scientific activity at the computer can be automated. This in turn lets scientists concentrate on the science rather than the repetitive handling of data through multiple tools and applications. So, increasingly, we see these scientific activities at the computer being 'programmed'. Some disciplines have created scripting solutions, perhaps adopting their favourite scripting languages and creating libraries to handle their discipline-specific data, while others adopt workflow systems which automate the processing of data through a series of processing stages.Taverna is one of many scientific workflow management systems (see Workflow Management Systems on page 2) and supports what we might describe as 'application-level workflows', as opposed to some other systems which focus on scheduling tasks across computing resources [1]. Emerging from the UK's e-Science programme, Taverna is used extensively by scientists a...

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Section: Know Your Usersmentioning

confidence: 99%

Software Design for Empowering Scientists

Roure

Goble

2009

IEEE Softw.

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“…Along with other projects [7], my Grid has developed more formal, programmatically accessible middleware, to enable transfer of information and composition of data and tool services into large workflows, addressing the real needs to the lab biologist [15]. This environment comprises of a number of different components including: 1) Soaplab-A toolkit for the presentation of legacy command line applications, which covers the majority of bioinformatics tools, as Web Services.…”

Section: The Application Of Service Orientated Architecturesmentioning

confidence: 99%

“…The my Grid project has been seeking to apply these technologies to the bioinformatics domain. To this end, it has contributed to the generation of a rich service layer, has built a workflow engine and workflow development environment [15].…”

Section: Introductionmentioning

confidence: 99%

Feta: A Light-Weight Architecture for User Oriented Semantic Service Discovery

Lord

Alper

Wroe

et al. 2005

Lecture Notes in Computer Science

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Abstract. Semantic Web Services offer the possibility of highly flexible web service architectures, where new services can be quickly discovered, orchestrated and composed into workflows. Most existing work has, however, focused on complex service descriptions for automated composition. In this paper, we describe the requirements from the bioinformatics domain which demand technically simpler descriptions, involving the user community at all levels. We describe our data model and lightweight semantic discovery architecture. We explain how this fits in the larger architecture of the my Grid project, which overall enables interoperability and composition across, disparate, autonomous, third-party services. Our contention is that such light-weight service discovery provides a good fit for user requirements of bioinformatics and possibly other domains.

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“…Conversely, MOBY-S, S-MOBY, and my Grid focus primarily on passing lightweight data-only messages from service to service, without defining the operations that can be invoked on any given data object (Wilkinson and Links, 2002;Stevens et al, 2004). Though the caBIO approach gives more programmatic power, focusing on a data-only messaging system seems to be more flexible and requires less centralized maintenance.…”

Section: The Solutionsmentioning

confidence: 99%

BioMOBY Successfully Integrates Distributed Heterogeneous Bioinformatics Web Services. The PlaNet Exemplar Case

et al. 2005

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The burden of noninteroperability between on-line genomic resources is increasingly the rate-limiting step in large-scale genomic analysis. BioMOBY is a biological Web Service interoperability initiative that began as a retreat of representatives from the model organism database community in September, 2001. Its long-term goal is to provide a simple, extensible platform through which the myriad of on-line biological databases and analytical tools can offer their information and analytical services in a fully automated and interoperable way. Of the two branches of the larger BioMOBY project, the Web Services branch (MOBY-S) has now been deployed over several dozen data sources worldwide, revealing some significant observations about the nature of the integrative biology problem; in particular, that Web Service interoperability in the domain of bioinformatics is, unexpectedly, largely a syntactic rather than a semantic problem. That is to say, interoperability between bioinformatics Web Services can be largely achieved simply by specifying the data structures being passed between the services (syntax) even without rich specification of what those data structures mean (semantics). Thus, one barrier of the integrative problem has been overcome with a surprisingly simple solution. Here, we present a nontechnical overview of the critical components that give rise to the interoperable behaviors seen in MOBY-S and discuss an exemplar case, the PlaNet consortium, where MOBY-S has been deployed to integrate the on-line plant genome databases and analytical services provided by a European consortium of databases and data service providers.

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Exploring Williams–Beuren syndrome using myGrid

Abstract: The (my)Grid software is available via http://www.mygrid.org.uk

Cited by 85 publications

References 16 publications

Software Design for Empowering Scientists

Software Design for Empowering Scientists

Feta: A Light-Weight Architecture for User Oriented Semantic Service Discovery

BioMOBY Successfully Integrates Distributed Heterogeneous Bioinformatics Web Services. The PlaNet Exemplar Case

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