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Benchmarking workflow discovery: a case study from bioinformatics
Author(s) -
Goderis Antoon,
Fisher Paul,
Gibson Andrew,
Tanoh Franck,
Wolstencroft Katy,
De Roure David,
Goble Carole
Publication year - 2009
Publication title -
concurrency and computation: practice and experience
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.309
H-Index - 67
eISSN - 1532-0634
pISSN - 1532-0626
DOI - 10.1002/cpe.1447
Subject(s) - workflow , computer science , benchmarking , workflow management system , data science , automation , workflow technology , world wide web , software engineering , engineering , database , mechanical engineering , business , marketing
Automation in science is increasingly marked by the use of workflow technology. The sharing of workflows through repositories supports the verifiability, 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 the current practices in workflow sharing, re‐use and discovery among 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 and the other relying on text clustering. Copyright © 2009 John Wiley & Sons, Ltd.