From Bio-jETI process models to native code

Anna Lena Lamprecht, Tiziana Margaria, Bernhard Steffen

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Bio-jETI is a framework for model-based, graphical development and execution of bioinformatics analysis processes. With the GeneSys code generation framework we can automatically compile the workflow models into native, stand-alone program code. We show via a phylogenetic analysis workflow designed by the DNA Data Bank of Japan (DDBJ) how we generate 6 variants of Java code from the corresponding process model realized in Bio-jETI. Performance measurements show that 1) the overall workflow execution time is dominated by the remote services it uses, and thus 2)all 6 variants are almost as fast as the handwritten Java of DDBJ. This way, we obtain efficient native code essentially without programming. Thus, we demonstrate in this paper that modelbased workflow development in Bio-jETI offers several advantages over manual implementation - including higher agility, greater transparency and better maintainability - without compromising the runtime performance.

Original languageEnglish
Title of host publicationProceedings - 2009 14th IEEE International Conference on Engineering of Complex Computer Systems, ICECCS 2009
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages95-101
Number of pages7
ISBN (Print)9780769537023
DOIs
Publication statusPublished - 2009
Externally publishedYes
Event2009 14th IEEE International Conference on Engineering of Complex Computer Systems, ICECCS 2009 - Potsdam, Germany
Duration: 2 Jun 20094 Jun 2009

Publication series

NameProceedings of the IEEE International Conference on Engineering of Complex Computer Systems, ICECCS
ISSN (Print)2770-8527
ISSN (Electronic)2770-8535

Conference

Conference2009 14th IEEE International Conference on Engineering of Complex Computer Systems, ICECCS 2009
Country/TerritoryGermany
CityPotsdam
Period2/06/094/06/09

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