47 research outputs found
Benchmarking Workflow Discovery: A Case Study From Bioinformatics
No full textAutomation in science is increasingly marked by the use of workflow technology. The sharing of workflows through repositories supports the verifability, reproducibility and extensibility of computational experiments. However, the subsequent discovery of workflows remains a challenge, both from a sociological and technological viewpoint. Based on a survey with participants from 19 laboratories, we investigate current practices in workflow sharing, re-use and discovery amongst life scientists chiefly using the Taverna workflow management system. To address their perceived lack of effective workflow discovery tools, we go on to develop benchmarks for the evaluation of discovery tools, drawing on a series of practical exercises. We demonstrate the value of the benchmarks on two tools: one using graph matching, the other relying on text clustering
Discovering Scientific Workflows: The myExperiment Benchmarks
No full textAutomation in science is increasingly marked by the use of workflow technology. The sharing of workflows through publication mechanisms or repositories supports the verifiability, reproducibility and extensibility of computational experiments. However, the subsequent discovery of workflows remains a challenge, both from a technological and sociological viewpoint. We investigate current practices in workflow sharing, re-use and discovery amongst life scientists chiefly using the Taverna workflow management system. The study draws on two key sources: (i) a survey of researchers drawn from 19 research labs and (ii) an analysis of scientists’ behaviour on the myExperiment social network site, designed to encourage workflow exchange. The results reveal a multi-modal approach to workflow discovery, based on a mix of search on the content of the workflow and its situated context. We go on to develop a benchmark specifically for the evaluation of workflow discovery and to demonstrate it on two example approaches
myExperiment: Defining the Social Virtual Research Environment
No full textThe myExperiment Virtual Research Environment supports the sharing of research objects used by scientists, such as scientific workflows. For researchers it is both a social infrastructure that encourages sharing and a platform for conducting research, through familiar user interfaces. For developers it provides an open, extensible and participative environment. We describe the design, implementation and deployment of myExperiment and suggest that its four capabilities - research objects, social model, open environment and actioning research - are necessary characteristics of an effective Virtual Research Environment for e-research and open science
Recycling workflows and services through discovery and reuse
No full textScientific workflows are becoming a valuable tool for scientists to capture and automate e-Science procedures. Their success brings the opportunity to publish, share, reuse and re-purpose this explicitly captured knowledge. Within the myGrid project, we have identified key resources that can be shared including complete workflows, fragments of workflows and constituent services. We have examined the alternative ways that these resources can be described by their authors (and subsequent users) and developed a unified descriptive model to support their later discovery. By basing this model on existing standards, we have been able to extend existing Web service and Semantic Web service infrastructure whilst still supporting the specific needs of the e-Scientist. The myGrid components enable a workflow lifecycle that extends beyond execution to include the discovery of previous relevant designs, the reuse of those designs and their subsequent publication. Experience with example groups of scientists indicates that this cycle is valuable. The growing number of workflows and services mean more work is needed to support the user in effective ranking of search results and to support the re-purposing process. Copyright © 2006 John Wiley & Sons, Ltd
Workflow re-use and discovery in bioinformatics
No full textScientists in many disciplines are increasingly faced with analysing a deluge of scientific data from sources scattered across the globe. Workflow techniques have the potential to become an important part of on-line experimentation as they allow scien-tists to describe and enact their experimental processes in a structured, repeatable andverifiable way.Given the availability of scientist-friendly workflow editors, scientists are moving away from cutting and pasting data between Web pages in favour of producing automated workflows based on Web services. An increasingly large pool of workflows is being shared and made available for re-use. The notion that these workflows and the experimental processes they represent are a useful, re-usable artifact in their own right is new. As a new phenomenon, scientific workflow re-use and discovery is not well understood and it is unclear whether and how it could be supported automatically.The thesis analyses the workflow re-use and discovery process based on surveys, interviews and user experiments with scientists and scientific programmers from different disciplines. We also analyse the impact of using multiple models of computationon workflow re-use. In particular, we show how some models of computation are better re-usable than others.Further, we capture and model scientist re-use and discovery behaviour when re-using data flow workflows from the bioinformatics domain. The result is a suite of human benchmarks of value to developers of workflow discovery techniques.Finally, the benchmarks enable us to evaluate a range of existing service discov-ery based techniques and novel workflow-structure based discovery techniques. Thetechniques vary in the language they work over (natural language or a Semantic Web language) and the level of workflow detail they process. The evaluation shows that performance of the workflow discovery techniques swings substantially depending ont he task in question. This argues in favour of a multi-varied approach that combines multiple techniques
The Design and Realisation of the myExperiment Virtual Research Environment for Social Sharing of Workflows
No full textIn this paper we suggest that the full scientific potential of workflows will be achieved through mechanisms for sharing and collaboration, empowering scientists to spread their experimental protocols and to benefit from those of others. To facilitate this process we have designed and built the myExperiment Virtual Research Environment for collaboration and sharing of workflows and experiments. In contrast to systems which simply make workflows available, myExperiment provides mechanisms to support the sharing of workflows within and across multiple communities. It achieves this by adopting a social web approach which is tailored to the particular needs of the scientist. We present the motivation, design and realisation of myExperiment
