Skip to main content

A Modeling Approach for Bioinformatics Workflows

  • 390 Accesses

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

This is a preview of subscription content, access via your institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • DOI: 10.1007/978-3-030-35151-9_11
  • Chapter length: 17 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
eBook
USD   59.99
Price excludes VAT (USA)
  • ISBN: 978-3-030-35151-9
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book
USD   79.99
Price excludes VAT (USA)
Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.

Notes

  1. 1.

    https://cf.gu.se/english/bioinformatics.

  2. 2.

    https://wcmtm.gu.se/research-groups/genomics-platform.

  3. 3.

    https://www.mentimeter.com.

References

  1. Al-alshuhai, A., Siewe, F.: An extension of UML activity diagram to model the behaviour of context-aware systems. In: 2015 IEEE International Conference on Computer and Information Technology; Ubiquitous Computing and Communications; Dependable, Autonomic and Secure Computing; Pervasive Intelligence and Computing, pp. 431–437. IEEE (2015)

    Google Scholar 

  2. Amstutz, P., et al.: Common workflow language, v1. 0 (2016)

    Google Scholar 

  3. Bastos, R.M., Ruiz, D.D.A.: Extending UML activity diagram for workflow modeling in production systems. In: Proceedings of the 35th Annual Hawaii International Conference on System Sciences, pp. 3786–3795. IEEE (2002)

    Google Scholar 

  4. Brooke, J.: SUS: a retrospective. J. Usability Stud. 8(2), 29–40 (2013)

    Google Scholar 

  5. Fernando, T., Gureev, N., Matskin, M., Zwick, M., Natschläger, T.: WorkflowDSL: scalable workflow execution with provenance for data analysis applications. In: 2018 IEEE 42nd Annual Computer Software and Applications Conference (COMPSAC), vol. 1, pp. 774–779. IEEE (2018)

    Google Scholar 

  6. de Figueroa, L.H.B., et al.: A modeling and elicitation approach for bioinformatics workflows: supporting material (2019). http://www.cse.chalmers.se/~jenho/BioinformaticsWorkflows/

  7. Güss, C.D.: What is going through your mind? Thinking aloud as a method in cross-cultural psychology. Front. Psychol. 9, 1292 (2018)

    CrossRef  Google Scholar 

  8. Harper, D., Thompson, A.R.: Qualitative Research Methods in Mental Health and Psychotherapy: A Guide for Students and Practitioners. Wiley, Hoboken (2011)

    CrossRef  Google Scholar 

  9. Hevner, A.R.: A three cycle view of design science research. Scand. J. Inf. Syst. 19(2), 4 (2007)

    Google Scholar 

  10. Kanwal, S., Lonie, A., Sinnott, R.O.: Digital reproducibility requirements of computational genomic workflows (2017)

    Google Scholar 

  11. Karim, M.R., Michel, A., Zappa, A., Baranov, P., Sahay, R., Rebholz-Schuhmann, D.: Improving data workflow systems with cloud services and use of open data for bioinformatics research. Brief. Bioinf. 19(5), 1035–1050 (2017)

    CrossRef  Google Scholar 

  12. Korherr, B., List, B.: Extending the UML 2 activity diagram with business process goals and performance measures and the mapping to BPEL. In: Roddick, J.F., et al. (eds.) ER 2006. LNCS, vol. 4231, pp. 7–18. Springer, Heidelberg (2006). https://doi.org/10.1007/11908883_4

    CrossRef  Google Scholar 

  13. Krishna, R., Elisseev, V., Antao, S.: BaaS - bioinformatics as a service. In: Mencagli, G., et al. (eds.) Euro-Par 2018. LNCS, vol. 11339, pp. 601–612. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-10549-5_47

    CrossRef  Google Scholar 

  14. Moody, D.: The “physics” of notations: toward a scientific basis for constructing visual notations in software engineering. IEEE Trans. Softw. Eng. 35(6), 756–779 (2009)

    CrossRef  Google Scholar 

  15. Moody, D.L., Heymans, P., Matulevicius, R.: Improving the effectiveness of visual representations in requirements engineering: an evaluation of i* visual syntax. In: 2009 17th IEEE International RE Conference, pp. 171–180. IEEE (2009)

    Google Scholar 

  16. OMG: OMG Unified Modeling Language (OMG UML), Superstructure, Version 2.4.1, August 2011. http://www.omg.org/spec/UML/2.4.1

  17. Peffers, K., Tuunanen, T., Rothenberger, M.A., Chatterjee, S.: A design science research methodology for information systems research. J. Manag. Inf. Syst. 24(3), 45–77 (2007)

    CrossRef  Google Scholar 

  18. Robertson, S., Robertson, J.: Mastering the Requirements Process: Getting Requirements Right. Addison-Wesley, Boston (2012)

    Google Scholar 

  19. Roux-Rouquié, M., Caritey, N., Gaubert, L., Rosenthal-Sabroux, C.: Using the unified modelling language (UML) to guide the systemic description of biological processes and systems. Biosystems 75(1–3), 3–14 (2004)

    CrossRef  Google Scholar 

  20. Smith, J.A.: Qualitative Psychology: A Practical Guide to Research Methods. Sage, Thousand Oaks (2015)

    Google Scholar 

  21. Spyrou, S., Bamidis, P., Pappas, K., Maglaveras, N.: Extending UML activity diagrams for workflow modelling with clinical documents in regional health information systems. In: Connecting Medical Informatics and Bioinformatics: Proceedings of the 19th Medical Informatics Europe Conference (MIE2005), pp. 1160–1165 (2005)

    Google Scholar 

  22. Stefanov, V., List, B., Korherr, B.: Extending UML 2 activity diagrams with business intelligence objects. In: Tjoa, A.M., Trujillo, J. (eds.) DaWaK 2005. LNCS, vol. 3589, pp. 53–63. Springer, Heidelberg (2005). https://doi.org/10.1007/11546849_6

    CrossRef  Google Scholar 

  23. Störrle, H.: Semantics of structured nodes in UML 2.0 activities. In: 2nd Nordic Workshop on UML, pp. 19–32 (2004)

    Google Scholar 

  24. Syriani, E., Ergin, H.: Operational semantics of UML activity diagram: an application in project management. In: 2012 Second IEEE International Workshop on Model-Driven Requirements Engineering (MoDRE), pp. 1–8. IEEE (2012)

    Google Scholar 

  25. Taherdoost, H.: Sampling methods in research methodology; how to choose a sampling technique for research (2016)

    Google Scholar 

Download references

Acknowledgements

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

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jennifer Horkoff .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and Permissions

Copyright information

© 2019 IFIP International Federation for Information Processing

About this paper

Verify currency and authenticity via CrossMark

Cite this paper

Heckmann Barbalho de Figueroa, L. et al. (2019). A Modeling Approach for Bioinformatics Workflows. In: Gordijn, J., Guédria, W., Proper, H. (eds) The Practice of Enterprise Modeling. PoEM 2019. Lecture Notes in Business Information Processing, vol 369. Springer, Cham. https://doi.org/10.1007/978-3-030-35151-9_11

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-35151-9_11

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-35150-2

  • Online ISBN: 978-3-030-35151-9

  • eBook Packages: Computer ScienceComputer Science (R0)