Software Design for Empowering Scientists

Scientific research is increasingly digital. Some activities, such as data analysis, search, and simulation, can be accelerated by letting scientists write workflows and scripts that automate routine activities. These capture pieces of the scientific method that scientists can share. The averna Workbench, a widely deployed scientific-workflow-management system, together with the myExperiment social Web site for sharing scientific experiments, follow six principles of designing software for adoption by scientists and six principles of user engagement

Towards a Semantic Grid Architecture

The Semantic Grid is an extension of the current Grid in which information and services are given well defined and explicitly represented meaning, better enabling computers and people to work in cooperation. In the last few years, several projects have embraced this vision and there are already successful pioneering applications that combine the strengths of the Grid and of semantic technologies. However, the Semantic Grid currently lacks a reference architecture, or a systematic approach for designing Semantic Grid components or applications. We need a Reference Semantic Grid Architecture that extends the Open Grid Services Architecture by explicitly defining the mechanisms that will allow for the explicit use of semantics and the associated knowledge to support a spectrum of service capabilities. An architecture would have (at least) three major components which are depicted in the extended abstract

Automatic vs Manual Provenance Abstractions: Mind the Gap

In recent years the need to simplify or to hide sensitive information in provenance has given way to research on provenance abstraction. In the context of scientific workflows, existing research provides techniques to semi automatically create abstractions of a given workflow description, which is in turn used as filters over the workflow's provenance traces. An alternative approach that is commonly adopted by scientists is to build workflows with abstractions embedded into the workflow's design, such as using sub-workflows. This paper reports on the comparison of manual versus semi-automated approaches in a context where result abstractions are used to filter report-worthy results of computational scientific analyses. Specifically; we take a real-world workflow containing user-created design abstractions and compare these with abstractions created by ZOOM UserViews and Workflow Summaries systems. Our comparison shows that semi-automatic and manual approaches largely overlap from a process perspective, meanwhile, there is a dramatic mismatch in terms of data artefacts retained in an abstracted account of derivation. We discuss reasons and suggest future research directions.Comment: Preprint accepted to the 2016 workshop on the Theory and Applications of Provenance, TAPP 201

Conceptual Linking: Ontology-based Open Hypermedia

This paper describes the attempts of the COHSE project to define and deploy a Conceptual Open Hypermedia Service. Consisting of • an ontological reasoning service which is used to represent a sophisticated conceptual model of document terms and their relationships; • a Web-based open hypermedia link service that can offer a range of different link-providing facilities in a scalable and non-intrusive fashion; and integrated to form a conceptual hypermedia system to enable documents to be linked via metadata describing their contents and hence to improve the consistency and breadth of linking of WWW documents at retrieval time (as readers browse the documents) and authoring time (as authors create the documents)

Conceptual Linking: Ontology-based Open Hypermedia

This paper describes the attempts of the COHSE project to define and deploy a Conceptual Open Hypermedia Service. Consisting of • an ontological reasoning service which is used to represent a sophisticated conceptual model of document terms and their relationships; • a Web-based open hypermedia link service that can offer a range of different link-providing facilities in a scalable and non-intrusive fashion; and integrated to form a conceptual hypermedia system to enable documents to be linked via metadata describing their contents and hence to improve the consistency and breadth of linking of WWW documents at retrieval time (as readers browse the documents) and authoring time (as authors create the documents)

Help me describe my data: A demonstration of the Open PHACTS VoID Editor

Abstract. The Open PHACTS VoID Editor helps non-Semantic Web experts to create machine interpretable descriptions for their datasets. The web app guides the user, an expert in the domain of the data, through a series of questions to capture details of their dataset and then generates a VoID dataset description. The generated dataset description conforms to the Open PHACTS dataset description guidelines that en-sure suitable provenance information is available about the dataset to enable its discovery and reuse

The Low Down on e-Science and Grids for Biology

The Grid is touted as a next generation Internet/Web, designed primarily to support e-Science. I hope to shed some light on what the Grid is, its purpose, and its potential impact on scientific practice in biology. The key message is that biologists are already primarily working in a manner that the Grid is intended to support. However, to ensure that the Grid’s good intentions are appropriate and fulfilled in practice, biologists must become engaged in the process of its development