A Modeling Approach for Bioinformatics Workflows

Conference paper
Part of the Lecture Notes in Business Information Processing book series (LNBIP, volume 369)


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.


UML Activity diagram Workflow Bioinformatics 



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


  1. 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. 2.
    Amstutz, P., et al.: Common workflow language, v1. 0 (2016)Google Scholar
  3. 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. 4.
    Brooke, J.: SUS: a retrospective. J. Usability Stud. 8(2), 29–40 (2013)Google Scholar
  5. 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. 6.
    de Figueroa, L.H.B., et al.: A modeling and elicitation approach for bioinformatics workflows: supporting material (2019).
  7. 7.
    Güss, C.D.: What is going through your mind? Thinking aloud as a method in cross-cultural psychology. Front. Psychol. 9, 1292 (2018)CrossRefGoogle Scholar
  8. 8.
    Harper, D., Thompson, A.R.: Qualitative Research Methods in Mental Health and Psychotherapy: A Guide for Students and Practitioners. Wiley, Hoboken (2011)CrossRefGoogle Scholar
  9. 9.
    Hevner, A.R.: A three cycle view of design science research. Scand. J. Inf. Syst. 19(2), 4 (2007)Google Scholar
  10. 10.
    Kanwal, S., Lonie, A., Sinnott, R.O.: Digital reproducibility requirements of computational genomic workflows (2017)Google Scholar
  11. 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)CrossRefGoogle Scholar
  12. 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). Scholar
  13. 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). Scholar
  14. 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)CrossRefGoogle Scholar
  15. 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. 16.
    OMG: OMG Unified Modeling Language (OMG UML), Superstructure, Version 2.4.1, August 2011.
  17. 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)CrossRefGoogle Scholar
  18. 18.
    Robertson, S., Robertson, J.: Mastering the Requirements Process: Getting Requirements Right. Addison-Wesley, Boston (2012)Google Scholar
  19. 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)CrossRefGoogle Scholar
  20. 20.
    Smith, J.A.: Qualitative Psychology: A Practical Guide to Research Methods. Sage, Thousand Oaks (2015)Google Scholar
  21. 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. 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). Scholar
  23. 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. 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. 25.
    Taherdoost, H.: Sampling methods in research methodology; how to choose a sampling technique for research (2016)Google Scholar

Copyright information

© IFIP International Federation for Information Processing 2019

Authors and Affiliations

  1. 1.University of GothenburgGothenburgSweden
  2. 2.Chalmers University of TechnologyGothenburgSweden

Personalised recommendations