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

I. Wassink, Matthijs Ooms, Pieter Neerincx, Gerrit C. van der Veer, Han Rauwerda, Jack A.M. Leunissen, Timo M. Breit, Antinus Nijholt, P.E. van der Vet

Research output: Chapter in Book/Report/Conference proceedingConference contributionAcademicpeer-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 languageUndefined
Title of host publicationInformation Technology in Bio- and Medical Informatics, ITBAM 2010
EditorsSami Khuri, Lenka Lhotská, Nadia Pisanti
Place of PublicationBerlin
PublisherSpringer
Pages1-15
Number of pages15
ISBN (Print)978-3-642-15019-7
DOIs
Publication statusPublished - 2010

Publication series

NameLecture Notes in Computer Science
PublisherSpringer Verlag
Volume6266
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Keywords

  • METIS-271014
  • HMI-IE: Information Engineering
  • EWI-18375
  • IR-72923

Cite this

Wassink, I., Ooms, M., Neerincx, P., van der Veer, G. C., Rauwerda, H., Leunissen, J. A. M., ... van der Vet, P. E. (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 (pp. 1-15). (Lecture Notes in Computer Science; Vol. 6266). Berlin: Springer. https://doi.org/10.1007/978-3-642-15020-3_1
Wassink, I. ; Ooms, Matthijs ; Neerincx, Pieter ; van der Veer, Gerrit C. ; Rauwerda, Han ; Leunissen, Jack A.M. ; Breit, Timo M. ; Nijholt, Antinus ; van der Vet, P.E. / e-BioFlow: Improving practical use of workflow systems in bioinformatics. Information Technology in Bio- and Medical Informatics, ITBAM 2010. 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.",
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author = "I. Wassink and Matthijs Ooms and Pieter Neerincx and {van der Veer}, {Gerrit C.} and Han Rauwerda and Leunissen, {Jack A.M.} and Breit, {Timo M.} and Antinus Nijholt and {van der Vet}, P.E.",
note = "10.1007/978-3-642-15020-3_1",
year = "2010",
doi = "10.1007/978-3-642-15020-3_1",
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series = "Lecture Notes in Computer Science",
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Wassink, I, Ooms, M, Neerincx, P, van der Veer, GC, Rauwerda, H, Leunissen, JAM, Breit, TM, Nijholt, A & van der Vet, PE 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. Lecture Notes in Computer Science, vol. 6266, Springer, Berlin, pp. 1-15. https://doi.org/10.1007/978-3-642-15020-3_1

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

Information Technology in Bio- and Medical Informatics, ITBAM 2010. 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 proceedingConference contributionAcademicpeer-review

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AU - Ooms, Matthijs

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AU - van der Veer, Gerrit C.

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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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Wassink I, Ooms M, Neerincx P, van der Veer GC, 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. Berlin: Springer. 2010. p. 1-15. (Lecture Notes in Computer Science). https://doi.org/10.1007/978-3-642-15020-3_1