e-BioFlow: Improving practical use of workflow systems in bioinformatics

Ingo Wassink; Matthijs Ooms; Pieter Neerincx; Gerrit van der Veer; Han Rauwerda; Jack A.M. Leunissen; Timo M. Breit; Anton Nijholt; Paul van der Vet

doi:10.1007/978-3-642-15020-3_1

e-BioFlow: Improving practical use of workflow systems in bioinformatics

Ingo Wassink, Matthijs Ooms, Pieter Neerincx, Gerrit van der Veer, Han Rauwerda, Jack A.M. Leunissen, Timo M. Breit, Anton Nijholt, Paul van der Vet

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Academic › peer-review

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Abstract

Workflow management systems (WfMSs) are useful tools for bioinformaticians. As experiences with using WfMSs accumulate, shortcomings of current systems become apparent. In this paper, we focus on practical issues that hinder WfMS users and that arise in the design and execution of workflows, and in access of web services. We present e-BioFlow, a workflow engine that demonstrates in which way a number of these problems can be solved. e-BioFlow offers an improved user interface, can deal with large data volumes, stores all provenance, and has a powerful provenance browser. e-BioFlow also offers the possibility to design and run workflows step by step, allowing its users an explorative research style.

Original language	English
Title of host publication	Information Technology in Bio- and Medical Informatics, ITBAM 2010
Subtitle of host publication	First International Conference, Bilbao, Spain, September 1-2, 2010. Proceedings
Editors	Sami Khuri, Lenka Lhotská, Nadia Pisanti
Place of Publication	Berlin
Publisher	Springer
Pages	1-15
Number of pages	15
ISBN (Electronic)	978-3-642-15020-3
ISBN (Print)	978-3-642-15019-7
DOIs	https://doi.org/10.1007/978-3-642-15020-3_1
Publication status	Published - 2010
Event	1st International Conference on Information, Technology in Bio- and Medical Informatics, ITBAM 2010 - Bilbao, Spain Duration: 1 Sep 2010 → 2 Sep 2010 Conference number: 1

Publication series

Name	Lecture Notes in Computer Science
Publisher	Springer Verlag
Volume	6266
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	1st International Conference on Information, Technology in Bio- and Medical Informatics, ITBAM 2010
Abbreviated title	ITBAM
Country	Spain
City	Bilbao
Period	1/09/10 → 2/09/10

Keywords

HMI-IE: Information Engineering
Large data volume
Improve practical
Composite task
Future generation computer system
Graphical browser

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10.1007/978-3-642-15020-3_1

Wassink2010e-bioflow
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Wassink, I., Ooms, M., Neerincx, P., van der Veer, G., Rauwerda, H., Leunissen, J. A. M., Breit, T. M., Nijholt, A., & van der Vet, P. (2010). e-BioFlow: Improving practical use of workflow systems in bioinformatics. In S. Khuri, L. Lhotská, & N. Pisanti (Eds.), Information Technology in Bio- and Medical Informatics, ITBAM 2010: First International Conference, Bilbao, Spain, September 1-2, 2010. Proceedings (pp. 1-15). (Lecture Notes in Computer Science; Vol. 6266). Springer. https://doi.org/10.1007/978-3-642-15020-3_1

Wassink, Ingo ; Ooms, Matthijs ; Neerincx, Pieter ; van der Veer, Gerrit ; Rauwerda, Han ; Leunissen, Jack A.M. ; Breit, Timo M. ; Nijholt, Anton ; van der Vet, Paul. / e-BioFlow : Improving practical use of workflow systems in bioinformatics. Information Technology in Bio- and Medical Informatics, ITBAM 2010: First International Conference, Bilbao, Spain, September 1-2, 2010. Proceedings. editor / Sami Khuri ; Lenka Lhotská ; Nadia Pisanti. Berlin : Springer, 2010. pp. 1-15 (Lecture Notes in Computer Science).

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abstract = "Workflow management systems (WfMSs) are useful tools for bioinformaticians. As experiences with using WfMSs accumulate, shortcomings of current systems become apparent. In this paper, we focus on practical issues that hinder WfMS users and that arise in the design and execution of workflows, and in access of web services. We present e-BioFlow, a workflow engine that demonstrates in which way a number of these problems can be solved. e-BioFlow offers an improved user interface, can deal with large data volumes, stores all provenance, and has a powerful provenance browser. e-BioFlow also offers the possibility to design and run workflows step by step, allowing its users an explorative research style.",

keywords = "HMI-IE: Information Engineering, Large data volume, Improve practical, Composite task, Future generation computer system, Graphical browser",

author = "Ingo Wassink and Matthijs Ooms and Pieter Neerincx and {van der Veer}, Gerrit and Han Rauwerda and Leunissen, {Jack A.M.} and Breit, {Timo M.} and Anton Nijholt and {van der Vet}, Paul",

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booktitle = "Information Technology in Bio- and Medical Informatics, ITBAM 2010",

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note = "1st International Conference on Information, Technology in Bio- and Medical Informatics, ITBAM 2010, ITBAM ; Conference date: 01-09-2010 Through 02-09-2010",

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Wassink, I, Ooms, M, Neerincx, P, van der Veer, G, Rauwerda, H, Leunissen, JAM, Breit, TM, Nijholt, A & van der Vet, P 2010, e-BioFlow: Improving practical use of workflow systems in bioinformatics. in S Khuri, L Lhotská & N Pisanti (eds), Information Technology in Bio- and Medical Informatics, ITBAM 2010: First International Conference, Bilbao, Spain, September 1-2, 2010. Proceedings. Lecture Notes in Computer Science, vol. 6266, Springer, Berlin, pp. 1-15, 1st International Conference on Information, Technology in Bio- and Medical Informatics, ITBAM 2010, Bilbao, Spain, 1/09/10. https://doi.org/10.1007/978-3-642-15020-3_1

e-BioFlow : Improving practical use of workflow systems in bioinformatics. / Wassink, Ingo; Ooms, Matthijs; Neerincx, Pieter; van der Veer, Gerrit; Rauwerda, Han; Leunissen, Jack A.M.; Breit, Timo M.; Nijholt, Anton; van der Vet, Paul.

Information Technology in Bio- and Medical Informatics, ITBAM 2010: First International Conference, Bilbao, Spain, September 1-2, 2010. Proceedings. ed. / Sami Khuri; Lenka Lhotská; Nadia Pisanti. Berlin : Springer, 2010. p. 1-15 (Lecture Notes in Computer Science; Vol. 6266).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Academic › peer-review

TY - GEN

T1 - e-BioFlow

T2 - 1st International Conference on Information, Technology in Bio- and Medical Informatics, ITBAM 2010

AU - Wassink, Ingo

AU - Ooms, Matthijs

AU - Neerincx, Pieter

AU - van der Veer, Gerrit

AU - Rauwerda, Han

AU - Leunissen, Jack A.M.

AU - Breit, Timo M.

AU - Nijholt, Anton

AU - van der Vet, Paul

N1 - Conference code: 1

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Y1 - 2010

N2 - Workflow management systems (WfMSs) are useful tools for bioinformaticians. As experiences with using WfMSs accumulate, shortcomings of current systems become apparent. In this paper, we focus on practical issues that hinder WfMS users and that arise in the design and execution of workflows, and in access of web services. We present e-BioFlow, a workflow engine that demonstrates in which way a number of these problems can be solved. e-BioFlow offers an improved user interface, can deal with large data volumes, stores all provenance, and has a powerful provenance browser. e-BioFlow also offers the possibility to design and run workflows step by step, allowing its users an explorative research style.

AB - Workflow management systems (WfMSs) are useful tools for bioinformaticians. As experiences with using WfMSs accumulate, shortcomings of current systems become apparent. In this paper, we focus on practical issues that hinder WfMS users and that arise in the design and execution of workflows, and in access of web services. We present e-BioFlow, a workflow engine that demonstrates in which way a number of these problems can be solved. e-BioFlow offers an improved user interface, can deal with large data volumes, stores all provenance, and has a powerful provenance browser. e-BioFlow also offers the possibility to design and run workflows step by step, allowing its users an explorative research style.

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KW - Large data volume

KW - Improve practical

KW - Composite task

KW - Future generation computer system

KW - Graphical browser

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DO - 10.1007/978-3-642-15020-3_1

M3 - Conference contribution

SN - 978-3-642-15019-7

T3 - Lecture Notes in Computer Science

SP - 1

EP - 15

BT - Information Technology in Bio- and Medical Informatics, ITBAM 2010

A2 - Khuri, Sami

A2 - Lhotská, Lenka

A2 - Pisanti, Nadia

PB - Springer

CY - Berlin

Y2 - 1 September 2010 through 2 September 2010

ER -

Wassink I, Ooms M, Neerincx P, van der Veer G, Rauwerda H, Leunissen JAM et al. e-BioFlow: Improving practical use of workflow systems in bioinformatics. In Khuri S, Lhotská L, Pisanti N, editors, Information Technology in Bio- and Medical Informatics, ITBAM 2010: First International Conference, Bilbao, Spain, September 1-2, 2010. Proceedings. Berlin: Springer. 2010. p. 1-15. (Lecture Notes in Computer Science). https://doi.org/10.1007/978-3-642-15020-3_1