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Benchmarking Workflow Discovery: A Case Study From Bioinformatics

Benchmarking Workflow Discovery: A Case Study From Bioinformatics
Benchmarking Workflow Discovery: A Case Study From Bioinformatics
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.
Scientific Workflow, Bioinformatics, Discovery, Benchmark, Taverna, myExperiment
Goderis, Antoon
ec60782c-4361-4ee3-85a7-379aeca96a67
Fisher, Paul
4c277313-566a-48dc-8b37-bff860c32904
Gibson, Andrew
8e4893ca-e598-4b4b-945a-67a3ca1e8024
Tanoh, Franck
8ff77403-306d-48df-8b75-59c6cbed68de
Wolstencroft, Katy
63a73df2-c820-4234-9753-3b5a9e249040
De Roure, David
02879140-3508-4db9-a7f4-d114421375da
Goble, Carole
8c248c0f-f19e-4dda-838b-77a89c5d3d38
Goderis, Antoon
ec60782c-4361-4ee3-85a7-379aeca96a67
Fisher, Paul
4c277313-566a-48dc-8b37-bff860c32904
Gibson, Andrew
8e4893ca-e598-4b4b-945a-67a3ca1e8024
Tanoh, Franck
8ff77403-306d-48df-8b75-59c6cbed68de
Wolstencroft, Katy
63a73df2-c820-4234-9753-3b5a9e249040
De Roure, David
02879140-3508-4db9-a7f4-d114421375da
Goble, Carole
8c248c0f-f19e-4dda-838b-77a89c5d3d38

Goderis, Antoon, Fisher, Paul, Gibson, Andrew, Tanoh, Franck, Wolstencroft, Katy, De Roure, David and Goble, Carole (2009) Benchmarking Workflow Discovery: A Case Study From Bioinformatics. Concurrency and Computation: Practice and Experience. (Submitted)

Record type: Article

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.

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More information

Submitted date: 15 February 2009
Keywords: Scientific Workflow, Bioinformatics, Discovery, Benchmark, Taverna, myExperiment
Organisations: Electronics & Computer Science

Identifiers

Local EPrints ID: 267107
URI: https://eprints.soton.ac.uk/id/eprint/267107
PURE UUID: 81cc9acb-b67c-4164-8f6d-cfcef3d36b11
ORCID for David De Roure: ORCID iD orcid.org/0000-0001-9074-3016

Catalogue record

Date deposited: 14 Feb 2009 20:08
Last modified: 06 Nov 2018 17:31

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