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A Modeling Approach for Bioinformatics Workflows

  • Laiz Heckmann Barbalho de Figueroa
  • Rema Salman
  • Jennifer HorkoffEmail author
  • Soni Chauhan
  • Marcela Davila
  • Francisco Gomes de Oliveira Neto
  • Alexander Schliep
Conference paper
Part of the Lecture Notes in Business Information Processing book series (LNBIP, volume 369)

Abstract

Bioinformaticians execute frequent, complex, manual and semi-scripted workflows to process data. There are many tools to manage and conduct these workflows, but there is no domain-specific way to textually and diagrammatically document them. Consequently, we create methods for modeling bioinformatics workflows. Specifically, we extend the Unified Modeling Language (UML) Activity Diagram to the bioinformatics domain by including domain-specific concepts and notations. Additionally, a template was created to document the same concepts in a text format. A design science methodology was followed, where four iterations with seven domain experts tailored the artefacts, extending concepts and improving usability, terminology, and notations. The UML extension received a positive evaluation from bioinformaticians. However, the written template was rejected due to the amount of text and complexity.

Keywords

UML Activity diagram Workflow Bioinformatics 

Notes

Acknowledgements

This work was supported by a Chalmers ICT Area of Advance SEED project and the Swedish Foundation for Strategic Research (RIF14–0081).

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Copyright information

© IFIP International Federation for Information Processing 2019

Authors and Affiliations

  • Laiz Heckmann Barbalho de Figueroa
    • 1
  • Rema Salman
    • 1
  • Jennifer Horkoff
    • 1
    • 2
    Email author
  • Soni Chauhan
    • 1
  • Marcela Davila
    • 1
  • Francisco Gomes de Oliveira Neto
    • 1
    • 2
  • Alexander Schliep
    • 1
    • 2
  1. 1.University of GothenburgGothenburgSweden
  2. 2.Chalmers University of TechnologyGothenburgSweden

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