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Benchmarking Workflow Discovery: A Case Study From Bioinformatics

Goderis, A., Fisher, P., Gibson, A., Tanoh, F., Wolstencroft, K., De Roure, D. and Goble, C. (2009) Benchmarking Workflow Discovery: A Case Study From Bioinformatics. Concurrency: Practice and Experience . ISSN 1040-3108 (In Press)

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Abstract

Automation 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.

Item Type:Article
Creator/Authors:
Antoon Goderis
Paul Fisher
Andrew Gibson
Franck Tanoh
Katy Wolstencroft
David De Roure
Carole Goble
Keywords:Scientific Workflow, Bioinformatics, Discovery, Benchmark, Taverna, myExperiment
Research Group:Old ECS Groups > Intelligence, Agents, Multimedia
ISSN:1040-3108
Date:15 February 2009
Information about this record:
Performance Indicator:EZ~07~01~11
Citations:ISI: 3, Google Scholar: 7
Downloads (2010):146
ID Code:17107
Last Modified:23 Sep 2011 10:37
Deposited On:14 Feb 2009 20:08 by De Roure, David

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References in Article

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