Advertisement

Scientific workflows with the jABC framework

A review after a decade in the field
  • Anna-Lena LamprechtEmail author
  • Bernhard Steffen
  • Tiziana Margaria
SW

Abstract

The jABC is a framework for process modelling and execution according to the XMDD (eXtreme model-driven design) paradigm, which advocates the rigorous use of user-level models in the software development process and software life cycle. We have used the jABC in the domain of scientific workflows for more than a decade now—an occasion to look back and take stock of our experiences in the field. On the one hand, we discuss results from the analysis of a sample of nearly 100 scientific workflow applications that have been implemented with the jABC. On the other hand, we reflect on our experiences and observations regarding the workflow development process with the framework. We then derive and discuss ongoing further developments and future perspectives for the framework, all with an emphasis on simplicity for end users through increased domain specificity. Concretely, we describe how the use of the PROPHETS synthesis plugin can enable a semantics-based simplification of the workflow design process, how with the jABC4 and DyWA frameworks more attention is paid to the ease of data management, and how the Cinco SCCE Meta-Tooling Suite can be used to generate tailored workflow management tools.

Keywords

Scientific workflows Model-driven design Workflow modeling Process modeling Loose programming Automatic workflow composition 

Notes

Acknowledgments

Many thanks go to our students and cooperation partners for all the scientific workflow applications that would not have been implemented without them. We also thank Alexander Wickert for his assistance in the process modelling courses and for his contributions to the service usage analysis functionality of jABCstats. This work was supported, in part, by Science Foundation Ireland Grant 13/RC/2094 and co-funded under the European Regional Development Fund through the Southern & Eastern Regional Operational Program to Lero—the Irish Software Research Centre (www.lero.ie).

References

  1. 1.
    Cinco SCCE Meta Tooling Suite. http://cinco.scce.info. last accessed 2 May 2016
  2. 2.
    DDBJ Web API for Biology. http://xml.nig.ac.jp/workflow/. temporarily suspended since 15 Feb 2012
  3. 3.
    OnlineHPC. http://onlinehpc.com/site/main. last accessed 15 Jan 2016
  4. 4.
    Pfam: RESTful interface. http://pfam.sanger.ac.uk/help#tabview=tab10. last accessed 9 Sept 2013
  5. 5.
    SCCE-service centered continuous engineering. http://scce.info. last accessed 26 Feb 2014
  6. 6.
    The R Project for Statistical Computing. http://www.r-project.org/. last accessed 5 May 2013
  7. 7.
    Al-areqi, S., Kriewald, S., Lamprecht, A.-L., Reusser, D., Wrobel, M., Margaria, T.: Agile workflows for climate impact risk assessment based on the ci:grasp platform and the jABC modeling framework. In: International environmental modelling and software society (iEMSs) 7th International Congress on Environmental Modelling and Software (2014) (accepted)Google Scholar
  8. 8.
    Alonso, G., Pautasso, C.: JOpera: a toolkit for efficient visual composition of web services. Int. J. Electron Commer. (IJEC) 9(2), 107–141 (2004)Google Scholar
  9. 9.
    Bajohr, M., Margaria, T.: MaTRICS: a service-based management tool for remote intelligent configuration of systems. Innov. Syst. Softw. Eng. (ISSE) 2(2), 99–111 (2005)CrossRefGoogle Scholar
  10. 10.
    Bajohr, M., Margaria, T.: High service availability in MaTRICS for the OCS. In: Margaria, T., Steffen, B. (eds.) Leveraging Applications of Formal Methods. Verification and Validation, vol. 17 of Communications in Computer and Information Science, pp. 572–586. Springer, Berlin (2008)Google Scholar
  11. 11.
    Bakera, M., Jörges, S., Margaria, T.: Test your strategy: graphical construction of strategies for connect-four. In: Proceedings of the 2009 14th IEEE international conference on engineering of complex computer systems. ICECCS ’09, pp. 172–181. IEEE Computer Society, Washington, DC, USA (2009)Google Scholar
  12. 12.
    Bakera, M., Margaria, T., Renner, C., Steffen, B.: Tool-supported enhancement of diagnosis in model-driven verification. Innov. Syst. Softw. Eng. 5, 211–228 (2009)CrossRefGoogle Scholar
  13. 13.
    Barnes, D., Kölling, M.: Objects First with Java: A Practical Introduction Using BlueJ. Pearson Education International, New York (2009)Google Scholar
  14. 14.
    Bau, D.: Pencil Code: A Programming Primer. Createspace Independent Pub (2013). https://book.pencilcode.net
  15. 15.
    Beck, K., Andres, C.: Extreme Programming Explained: Embrace Change. Addison-Wesley Professional, Boston (2004)Google Scholar
  16. 16.
    Bevan, N., Blom, J., Blythe, M., Buie, E., Christou, G., Cockton, G., Diefenbach, S., Gilmore, D., Hartmann, J., Hassenzahl, M., Höök, K., Hornbaek, K., Karapanos, E., Kaye, J., Keinonen, T., Kilbourn, K., Kort, J., Kowalkiewicz, M., Kurosu, M., Kuutti, K., Mahlke, S., McClelland, I., Mulder, I., Rozendaal, M., Tractinsky, N., Väänänen-Vainio-Mattila, K., Kuijk, J.V., van Schaik, P., Visch, V., Wright, P.: User experience white paper-bringing clarity to the concept of user experience. http://www.allaboutux.org/files/UX-WhitePaper.pdf. Result from Dagstuhl Seminar on Demarcating User Experience, September 15–18, 2010 (2011)
  17. 17.
    Bhagat, J., Tanoh, F., Nzuobontane, E., Laurent, T., Orlowski, J., Roos, M., Wolstencroft, K., Aleksejevs, S., Stevens, R., Pettifer, S., Lopez, R., Goble, C.A.: BioCatalogue: a universal catalogue of web services for the life sciences. Nucleic Acids Res. 38(supp\(\_\)2), W689–694 (2010)Google Scholar
  18. 18.
    Blankenberg, D., Von Kuster, G., Coraor, N., Ananda, G., Lazarus, R., Mangan, M., Nekrutenko, A., Taylor, J.: Galaxy: a web-based genome analysis tool for experimentalists. In: Ausubel, F.M., et al. (eds.) Current Protocols in Molecular Biology, chapter 19. Wiley, New York, January (2010)Google Scholar
  19. 19.
    Blum, N., Magedanz, T., Kleessen, J., Margaria, T.: Enabling eXtreme model driven design of parlay X-based communications services for end-to-end multiplatform service orchestrations. In: Engineering of complex computer systems, 2009 14th IEEE international conference on, pp. 240–247, June (2009)Google Scholar
  20. 20.
    Bordihn, H., Lamprecht, A.-L., Margaria, T.: Foundations of semantics and model checking in a software engineering course. In: Bollin, A., Margaria, T., Perseil, I. (eds.) Proceedings of the first workshop on formal methods in software engineering education and training (FMSEE&T ’15), vol. 1385, pp. 19–26. CEUR Workshop Proceedings (2015)Google Scholar
  21. 21.
    Borner, J.: A molecular approach to chelicerate phylogeny. Diploma thesis, Universität Hamburg (2010)Google Scholar
  22. 22.
    Callahan, S., Freire, J., Santos, E., Scheidegger, C., Silva, C., Vo, H.: Managing the evolution of dataflows with visTrails. In: Data engineering workshops, 2006. Proceedings. 22nd international conference on, pp. 71–71 (2006)Google Scholar
  23. 23.
    Carriero, N.J., Gelernter, D., Mattson, T.G., Sherman, A.H.: The Linda Alternative to Message-passing Systems. Parallel Comput. 20(4), 633–655 (1994)CrossRefzbMATHGoogle Scholar
  24. 24.
    Clarke, E.M., Grumberg, O., Peled, D.A.: Model Checking. The MIT Press, Cambridge (1999)Google Scholar
  25. 25.
    Cleaveland, R., Parrow, J., Steffen, B.: The concurrency workbench: a semantics-based tool for the verification of concurrent systems. ACM Trans. Program. Lang. Syst. 15(1), 36–72 (1993)CrossRefGoogle Scholar
  26. 26.
    Curcin, V., Ghanem, M., Guo, Y.: Analysing scientific workflows with computational tree logic. Clust. Comput. 12, 399–419 (2009)CrossRefGoogle Scholar
  27. 27.
    Deelman, E., Singh, G., Hui Su, M., Blythe, J., Gil, A., Kesselman, C., Mehta, G., Vahi, K., Berriman, G.B., Good, J., Laity, A., Jacob, J.C., Katz, D.S.: Pegasus: a framework for mapping complex scientific workflows onto distributed systems. Sci. Program. J. 13:219–237 (2005)Google Scholar
  28. 28.
    DiBernardo, M., Pottinger, R., Wilkinson, M.: Semi-automatic web service composition for the life sciences using the BioMoby semantic web framework. J. Biomed. Inform. 41(5), 837–847 (2008)CrossRefGoogle Scholar
  29. 29.
    Ebert, B.E., Lamprecht, A.-L., Steffen, B., Blank, L.M.: Flux-P: automating metabolic flux analysis. Metabolites 2(4), 872–890 (2012)CrossRefGoogle Scholar
  30. 30.
    Eker, J., Janneck, J., Lee, E., Liu, J., Liu, X., Ludvig, J., Neuendorffer, S., Sachs, S., Xiong, Y.: Taming heterogeneity-the Ptolemy approach. Proc. IEEE 91(1), 127–144 (2003)CrossRefGoogle Scholar
  31. 31.
    Frohme, M.: Agile Domänenmodellierung für prozessgesteuerte Webanwendungen. Bachelor thesis, TU Dortmund (2013)Google Scholar
  32. 32.
    Garijo, D., Alper, P., Belhajjame, K., Corcho O., Gil, Y., Goble, C.: Common motifs in scientific workflows: an empirical analysis. Future Gener. Comput. Syst. (2013) (In press)Google Scholar
  33. 33.
    Ghanem, M., Curcin, V., Wendel, P., Guo, Y.: Building and Using Analytical Workflows in Discovery Net, pp. 119–139. Wiley, New York (2009)Google Scholar
  34. 34.
    Giegerich, R., Meyer, F., Schleiermacher, C.: GeneFisher-software support for the detection of postulated genes. Proc. Int. Conf. Intell. Syst. Mol. Biol. (ISMB) 4, 68–77 (1996)Google Scholar
  35. 35.
    Gil, Y., Ratnakar, V., Deelman, E., Mehta, G., Kim, J.: Wings for Pegasus: creating large-scale scientific applications using semantic representations of computational workflows. In: Proceedings of the 19th national conference on Innovative applications of artificial intelligence-Vol. 2, pp. 1767–1774. AAAI Press (2007)Google Scholar
  36. 36.
    Goble, C.A., Bhagat, J., Aleksejevs, S., Cruickshank, D., Michaelides, D., Newman, D., Borkum, M., Bechhofer, S., Roos, M., Li, P., Roure, D.D.: myExperiment: a repository and social network for the sharing of bioinformatics workflows. Nucl. Acids Res. 38(suppl\(\_\)2), W677–682 (2010)Google Scholar
  37. 37.
    Hagemeier, D.: GeneFisher2-an AJAX based implementation of GeneFisher-P. Bachelor’s thesis, University Bielefeld, Faculty of Technology, Dec. (2006)Google Scholar
  38. 38.
    Hörmann, M., Margaria, T., Mender, T., Nagel, R., Steffen, B., Trinh, H.: The jABC approach to rigorous collaborative development of SCM applications. In: Margaria, T., Steffen, B. (eds.) Leveraging Applications of Formal Methods. Verification and Validation, vol. 17 of communications in computer and information science, pp. 724–737. Springer, Berlin (2008)Google Scholar
  39. 39.
    Huhns, M.N., Singh, M.P.: Service-oriented computing: key concepts and principles. IEEE Internet Comput. 9, 75–81 (2005)CrossRefGoogle Scholar
  40. 40.
    Hull, D., Wolstencroft, K., Stevens, R., Goble, C., Pocock, M.R., Li, P., Oinn, T.: Taverna: a tool for building and running workflows of services. Nuc. Acids Res. 34(Web Server):W729–W732 (2006)Google Scholar
  41. 41.
    Isberner, M., Howar, F., Steffen, B.: Learning register automata: from languages to program structures. Mach. Learn. 96(1), 65–98 (2014). doi: 10.1007/s10994-013-5419-7
  42. 42.
    Ison, J., Kalaš, M., Jonassen, I., Bolser, D., Uludag, M., McWilliam, H., Malone, J., Lopez, R., Pettifer, S., Rice, P.: EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics (2013)Google Scholar
  43. 43.
    Jarvis, A., Reuter, H., Nelson, A., Guevara, E.: Hole-filled SRTM for the globe Version 4 last accessed 7 Mar 2014 (2008)Google Scholar
  44. 44.
    Jonsson, B., Margaria, T., Naeser, G., Nyström, J., Steffen, B.: Incremental requirement specification for evolving systems. Nord. J. Comput. 8, 65–87 (2001)zbMATHGoogle Scholar
  45. 45.
    Jörges, S.: Construction and Evolution of Code Generators-A Model-Driven and Service-Oriented Approach. Lecture Notes in Computer Science, vol. 7747. Springer, Berlin (2013)Google Scholar
  46. 46.
    Jörges, S., Lamprecht, A.-L., Margaria, T., Schaefer, I., Steffen, B.: A Constraint-based variability modeling framework. Int. J. Softw. Tools Technol. Transf. (STTT) 14(5), 511–530 (2012)CrossRefGoogle Scholar
  47. 47.
    Jörges, S., Margaria, T., Steffen, B.: Genesys: service-oriented construction of property conform code generators. Innov. Syst. Softw. Eng. 4(4), 361–384 (2008)CrossRefGoogle Scholar
  48. 48.
    Karlsson, J., Martín-Requena, V., Ríos, J., Trelles, O.: Workflow composition and enactment using jORCA. In: Margaria, T., Steffen, B. (eds.) Leveraging Applications of Formal Methods. Verification, and Validation, vol. 6415 of Lecture Notes in Computer Science, pp. 328–339. Springer, Berlin (2010)Google Scholar
  49. 49.
    Kiczales, G., Lamping, J., Mendhekar, A., Maeda, C., Lopes, C., Loingtier, J.-M., Irwin, J.: Aspect-oriented programming. In: Akşit, M., Matsuoka, S. (eds.) ECOOP’97-Object-Oriented Programming. Lecture Notes in Computer Science, vol. 1241, pp. 220–242. Springer, Berlin (1997)Google Scholar
  50. 50.
    Kriewald, S.: srtmtools: SRTM tools. R package version 1, 2013–00 (2013)Google Scholar
  51. 51.
    Kubczak, C., Margaria, T., Fritsch, A., Steffen, B.: Biological LC/MS Preprocessing and Analysis with jABC, jETI and xcms. In: Proceedings of the 2nd international symposium on leveraging applications of formal methods, verification and validation (ISoLA 2006): 15–19 November 2006, Paphos, Cyprus, pp. 308–313. IEEE Computer Society (2006)Google Scholar
  52. 52.
    Kubczak, C., Margaria, T., Steffen, B., Nagel, R.: Service-oriented Mediation with jABC/jETI (2008)Google Scholar
  53. 53.
    Kubczak, C., Margaria, T., Steffen, B., Naujokat, S.: Service-oriented mediation with jETI/jABC: verification and export. In: Proceedings of the 2007 IEEE/WIC/ACM international conference on web intelligence and intelligent agent technology, WI-IAT workshop, pp. 144–147, Silicon Valley, California, USA, Nov. 2007. IEEE Computer Society Press (2007)Google Scholar
  54. 54.
    Lamprecht, A.-L.: User-Level Workflow Design-A Bioinformatics Perspective, volume 8311 of Lecture Notes in Computer Science. Springer (2013)Google Scholar
  55. 55.
    Lamprecht, A.-L., Margaria, T.: Scientific Workflows: Eternal Components, Changing Interfaces, Varying Compositions. In: Margaria, T., Steffen, B., Merten, M. (eds.) ISoLA 2012, Part I, vol. 7609 of LNCS, pp. 47–63. Springer, Berlin (2012)Google Scholar
  56. 56.
    Lamprecht, A.-L., Margaria, T. (eds.): Process Design for Natural Scientists-An Agile Model-Driven Approach. Communications in Computer and Information Science (CCIS), vol. 500. Springer, Berlin (2014)Google Scholar
  57. 57.
    Lamprecht, A.-L., Margaria, T.: Scientific workflows with XMDD: a way to use process modeling in computational science education. Procedia Computer Science, 51(0):1927–1936 (2015) (15th International Conference On Computational Science (ICCS 2015): Computational Science at the Gates of Nature)Google Scholar
  58. 58.
    Lamprecht, A.-L., Margaria, T., Steffen, B.: Seven variations of an alignment workflow–an illustration of agile process design and management in Bio-jETI. In: Mandoiu, I., Sunderraman, R., Zelikovsky, A. (eds.) Bioinformatics research and applications, vol. 4983 of Lecture Notes in Bioinformatics, pp. 445–456. Springer, Atlanta, Georgia (2008)Google Scholar
  59. 59.
    Lamprecht, A.-L., Margaria, T., Steffen, B.: Supporting process development in bio-jETI by model checking and synthesis. In: Semantic web applications and tools for life sciences (SWAT4LS 2009). CEUR workshop proceedings, vol. 435 (2008)Google Scholar
  60. 60.
    Lamprecht, A.-L., Margaria, T., Steffen, B.: Bio-jETI: a framework for semantics-based service composition. BMC Bioinform. 10(Suppl 10), S8 (2009)CrossRefGoogle Scholar
  61. 61.
    Lamprecht, A.-L., Margaria, T., Steffen, B.: Bioinformatics: processes and workflows. In: Laplante, P.A. (ed.) Encyclopedia of Software Engineering, chapter 13, pp. 118–130. Taylor & Francis, Abingdon, 11 (2010). doi: 10.1081/E-ESE-120044612
  62. 62.
    Lamprecht, A.-L., Margaria, T., Steffen, B., Sczyrba, A., Hartmeier, S., Giegerich, R.: GeneFisher-P: variations of GeneFisher as processes in Bio-jETI. BMC Bioinform. 9(Suppl 4), S13 (2008)CrossRefGoogle Scholar
  63. 63.
    Lamprecht, A.-L., Naujokat, S., Margaria, T., Steffen, B.: Synthesis-based loose programming. In: Proceedings of the 7th international conference on the quality of information and communications technology (QUATIC 2010). Porto, Portugal, pp. 262–267. IEEE, Sept (2010)Google Scholar
  64. 64.
    Lamprecht, A.-L., Naujokat, S., Margaria, T., Steffen, B.: Semantics-based composition of EMBOSS services. J. Biomed. Semant. 2(Suppl 1), S5 (2011)CrossRefGoogle Scholar
  65. 65.
    Lamprecht, A.-L., Naujokat, S., Steffen, B., Margaria, T.: Constraint-guided workflow composition based on the EDAM ontology. In: Burger, A., Marshall, M.S., Romano, P., Paschke, A., Splendiani, A. (eds.) Proceedings of the 3rd international workshop on semantic web applications and tools for life sciences (SWAT4LS 2010), vol. 698. CEUR Workshop Proceedings, December (2010)Google Scholar
  66. 66.
    Lis, M.: Workflow for phylogenetic tree construction. In: Lamprecht, A.-L., Margaria, T. (eds.) Process design for natural scientists: an agile model-driven approach, vol. 500 of CCIS. Springer, Berlin (2014)Google Scholar
  67. 67.
    Littauer, R., Ram, K., Ludäscher, B., Michener, W., Koskela, R.: Trends in use of scientific workflows: insights from a public repository and recommendations for best practices. In: 7th international digital curation conference (2011)Google Scholar
  68. 68.
    Ludäscher, B., Altintas, I., Berkley, C., Higgins, D., Jaeger, E., Jones, M., Lee, E.A., Tao, J., Zhao, Y.: Scientific workflow management and the Kepler systems. Concurr. Comput. Pract. Exp. 18(10), 1039–1065 (2006)CrossRefGoogle Scholar
  69. 69.
    Margaria, T.: Service is in the eyes of the beholder. IEEE Computer, Nov. (2007)Google Scholar
  70. 70.
    Margaria, T., Boßelmann, S., Doedt, M., Floyd, B.D., Steffen, B.: Customer-oriented business process management: visions and obstacles. In: Hinchey, M., Coyle, L. (eds.) Conquering Complexity, pp. 407–429. Springer, London (2012)CrossRefGoogle Scholar
  71. 71.
    Margaria, T., Floyd, B., Lamprecht, A.-L., Camargo, R.G., Neubauer, J., Seelaender, M.: Simple management of high assurance data in long-lived interdisciplinary healthcare research: a proposal. In: Margaria, T., Steffen, B. (eds.) ISoLA 2014, vol. 8803 of LNCS. Springer, Berlin (2014)Google Scholar
  72. 72.
    Margaria, T., Floyd, B.D., Steffen, B.: IT simply works: simplicity and embedded systems design. In: IEEE 35th annual computer software and applications conference workshops (COMPSACW), 2011, pp. 194–199, July (2011)Google Scholar
  73. 73.
    Margaria, T., Karusseit, M.: Community usage of the online conference service: an experience report from three CS conferences. In: Proceedings of the IFIP conference on towards the knowledge society: e-commerce. e-business, e-government, pp. 497–511. Kluwer, B.V., Deventer, The Netherlands (2002)Google Scholar
  74. 74.
    Margaria, T., Kubczak, C., Njoku, M., Steffen, B.: Model-based design of distributed collaborative bioinformatics processes in the jABC. In: Proceedings of the 11th IEEE international conference on engineering of complex computer systems (ICECCS’06), pp. 169–176. IEEE Computer Society, Los Alamitos, CA, USA, Aug. (2006)Google Scholar
  75. 75.
    Margaria, T., Kubczak, C., Steffen, B.: Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes. BMC Bioinform. 9(Suppl 4), S12 (2008)CrossRefGoogle Scholar
  76. 76.
    Margaria, T., Nagel, R., Steffen, B.: jETI: a tool for remote tool integration. In: Tools and algorithms for the construction and analysis of systems, vol. 3440/2005 of LNCS, pp. 557–562. Springer, Berlin/Heidelberg (2005)Google Scholar
  77. 77.
    Margaria, T., Steffen, B.: Backtracking-free design planning by automatic synthesis in METAFrame. In: Proceedings of 1st international conference on fundamental approaches to software engineering (FASE 1998), Lisbon, Portugal, pp. 188–204 (1998)Google Scholar
  78. 78.
    Margaria, T., Steffen, B.: Agile IT: thinking in user-centric models. In: Margaria, T., Steffen, B. (eds.) Leveraging applications of formal methods. Verification and validation, vol. 17 of communications in computer and information science, pp. 490–502. Springer, Berlin (2009)Google Scholar
  79. 79.
    Margaria, T., Steffen, B.: Business process modelling in the jABC: the one-thing-approach. In: Cardoso, J., van der Aalst, W. (eds.) Handbook of Research on Business Process Modeling. IGI Global, Pennsylvania (2009)Google Scholar
  80. 80.
    Margaria, T., Steffen, B.: Continuous model-driven engineering. IEEE. Comput. 42(10), 106–109 (2009)Google Scholar
  81. 81.
    Margaria, T., Steffen, B.: Simplicity as a driver for agile innovation. Computer 43(6), 90–92 (2010)CrossRefGoogle Scholar
  82. 82.
    Margaria, T., Steffen, B.: Service-orientation: conquering complexity with XMDD. In: Hinchey, M., Coyle, L. (eds.) Conquering Complexity, pp. 217–236. Springer, London (2012)CrossRefGoogle Scholar
  83. 83.
    Margaria, T., Steffen, B., Reitenspieß, M.: Service-oriented design: the roots. In: Proc. of the 3rd Int. Conf. on service-oriented computing (ICSOC 2005), Amsterdam, The Netherlands, vol. 3826 of LNCS, pp. 450–464. Springer, Berlin (2005)Google Scholar
  84. 84.
    Martín-Requena, V., Ríos, J., García, M., Ramírez, S., Trelles, O.: jORCA: easily integrating bioinformatics web services. Bioinformatics 26(4), 553–559 (2010)CrossRefGoogle Scholar
  85. 85.
    McCabe, T.J.: A complexity measure. IEEE Trans. Softw. Eng. SE-2(4):308–320, Dec 1976Google Scholar
  86. 86.
    Migliorini, S., Gambini, M., Rosa, M.L., ter Hofstede, A.H.M.: Pattern-based evaluation of scientific workflow management systems (2011). http://eprints.qut.edu.au/39935/
  87. 87.
    Müller-Olm, M., Schmidt, D., Steffen, B.: Model-checking-a tutorial introduction. In: Proceedings of the 6th international symposium on static analysis (SAS ’99), pp. 330–354 (1999)Google Scholar
  88. 88.
    Naujokat, S., Lamprecht, A.-L., Steffen, B.: Loose programming with PROPHETS. In: de Lara, J., Zisman, A. (eds.) Proc. of the 15th Int. Conf. on fundamental approaches to software engineering (FASE 2012), Tallinn, Estonia, vol. 7212 of LNCS, pp. 94–98. Springer, Heidelberg (2012)Google Scholar
  89. 89.
    Naujokat, S., Lybecait, M., Kopetzki, D., Steffen, B.: CINCO: a simplicity-driven approach to full generation of domain-specific graphical modeling tools (2015) (to appear)Google Scholar
  90. 90.
    Naujokat, S., Lybecait, M., Steffen, B., Kopetzki, D., Margaria, T.: Full generation of domain-specific graphical modeling tools: a meta\(^2\)modeling approach. (2015) (under submission)Google Scholar
  91. 91.
    Naujokat, S., Traonouez, L.-M., Isberner, M., Steffen, B., Legay, A.: Domain-specific code generator modeling: a case study for multi-faceted concurrent systems. In: Proc. of the 6th Int. Symp. on leveraging applications of formal methods, verification and validation, Part I (ISoLA 2014), vol. 8802 of LNCS, pp 463–480. Springer, Berlin (2014)Google Scholar
  92. 92.
    Neubauer, J.: Higher-order process engineering. Phd thesis, Technische Universität Dortmund (2014)Google Scholar
  93. 93.
    Neubauer, J.: Higher-order process engineering: The technical background. Technical report, Technische Universität Dortmund, April (2014)Google Scholar
  94. 94.
    Neubauer, J., Frohme, M., Steffen, B., Margaria, T.: Prototype-driven development of web applications with DyWA. In: Proc. of the 6th Int. Symp. on leveraging applications of formal methods, verification and validation, Part I (ISoLA 2014), number 8802 in LNCS, pp. 56–72. Springer, Berlin (2014)Google Scholar
  95. 95.
    Neubauer, J., Margaria, T., Steffen, B.: Design for verifiability: the OCS case study. In: Formal methods for industrial critical systems: a survey of applications, chapter 8, pp. 153–178. Wiley-IEEE Computer Society Press, Mar. (2013)Google Scholar
  96. 96.
    Neubauer, J., Steffen, B., Margaria, T.: Higher-order process modeling: product-lining, variability modeling and beyond. Electron. Proc. Theor. Comput. Sci. 129, 259–283 (2013)CrossRefGoogle Scholar
  97. 97.
    Oinn, T., Greenwood, M., Addis, M., Alpdemir, M.N., Ferris, J., Glover, K., Goble, C., Goderis, A., Hull, D., Marvin, D., Li, P., Lord, P., Pocock, M.R., Senger, M., Stevens, R., Wipat, A., Wroe, C.: Taverna: lessons in creating a workflow environment for the life sciences: research articles. Concurr. Comput. Pract. Exp. 18(10), 1067–1100 (2006)CrossRefGoogle Scholar
  98. 98.
    Qin, J., Fahringer, T.: Scientific Workflows-Programming, Optimization, and Synthesis with ASKALON and AWDL. Springer, Berlin (2012)zbMATHGoogle Scholar
  99. 99.
    Resnick, M., Maloney, J., Hernández, A.M., Rusk, N., Eastmond, E., Brennan, K., Millner, A., Rosenbaum, E., Silver, J., Silverman, B., Kafai, Y.: Scratch: programming for All. Commun. ACM 52(11), 60–67 (2009)CrossRefGoogle Scholar
  100. 100.
    Reso, J.: Protein classification workflow. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists: An Agile Model-Driven Approach, vol. 500 of CCIS. Springer, Berlin (2014)Google Scholar
  101. 101.
    Schmidt, D.C.: Guest editor’s introduction: model-driven engineering. IEEE Comput. 39(2), 25–31 (2006)CrossRefGoogle Scholar
  102. 102.
    Schütt, C.: Identification of differentially expressed genes. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists: An Agile Model-Driven Approach, vol. 500 of CCIS. Springer, Berlin (2014)Google Scholar
  103. 103.
    Simon, M.: Automatisierte Konstruktion thematischer Karten-Kartentypen, Prozessdefinition und Prozesssteuerung. Master’s thesis., University of Potdam (2014)Google Scholar
  104. 104.
    Smith, C.A., Want, E.J., O’Maille, G., Abagyan, R., Siuzdak, G.: XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal. Chem. 78(3), 779–787 (2006)CrossRefGoogle Scholar
  105. 105.
    Ståhl, D., Bosch, J.: Modeling continuous integration practice differences in industry software development. J. Syst. Softw. 87, 48–59 (2014)CrossRefGoogle Scholar
  106. 106.
    Steffen, B., Howar, F., Merten, M.: Introduction to active automata learning from a practical perspective. In: Bernardo, M., Issarny, V. (eds.) Formal Methods for Eternal Networked Software Systems. Lecture Notes in Computer Science, vol. 6659, pp. 256–296. Springer, Berlin (2011)CrossRefGoogle Scholar
  107. 107.
    Steffen, B., Margaria, T.: METAFrame in practice: design of intelligent network services. In: Olderog, E.-R., Steffen, B. (eds.) Correct System Design, vol. 1710 of Lecture Notes in Computer Science, pp. 390–415. Springer, Berlin (1999)Google Scholar
  108. 108.
    Steffen, B., Margaria, T., Braun, V.: The electronic tool integration platform: concepts and design. Int. J. Softw. Tools Technol. Transf. (STTT) 1(1–2), 9–30 (1997)CrossRefzbMATHGoogle Scholar
  109. 109.
    Steffen, B., Margaria, T., Braun, V., Kalt, N.: Hierarchical service definition. Annu. Rev. Commun. ACM 51, 847–856 (1997)Google Scholar
  110. 110.
    Steffen, B., Margaria, T., Claßen, A., Braun, V.: The METAFrame’95 environment. In: CAV, pp. 450–453 (1996)Google Scholar
  111. 111.
    Steffen, B., Margaria, T., Claßen, A., Braun, V.: Incremental formalization: a key to industrial success. Softw. Concepts Tools 17(2), 78–95 (1996)Google Scholar
  112. 112.
    Steffen, B., Margaria, T., Freitag, B.: Module configuration by minimal model construction. Technical report, Fakultät für Mathematik und Informatik, Universität Passau (1993)Google Scholar
  113. 113.
    Steffen, B., Margaria, T., Nagel, R., Jörges, S., Kubczak, C.: Model-driven development with the jABC. In: Bin, E., Ziv, A., Ur, S. (eds.) Hardware and Software. Verification and Testing, vol. 4383 of Lecture Notes in Computer Science, pp. 92–108. Springer, Berlin (2007)Google Scholar
  114. 114.
    Steffen, B., Margaria, T., von der Beeck, M.: Automatic synthesis of linear process models from temporal constraints: an incremental approach. In: ACM/SIGPLAN international workshop on automated analysis of software (AAS’97) (1997)Google Scholar
  115. 115.
    Steffen, B., Margaria, T., Wagner, C.: Round-Trip Engineering, chapter 96, pp. 1044–1055. Taylor & Francis, Abingdon (2010). doi: 10.1081/E-ESE-120044648
  116. 116.
    Taylor, I., Shields, M., Wang, I., Harrison, A.: The triana workflow environment: architecture and applications. In: Workflows for e-Science, chapter 20, pp. 320–339. Springer, New York, Secaucus, NJ, USA (2007)Google Scholar
  117. 117.
    van der Aalst, W.M.P., Pesic, M.: DecSerFlow: Towards a truly declarative service flow language. In: Web Services and Formal Methods. Third International Workshop, vol. 4184 of Lecture Notes in Computer Science, pp. 1–23. Springer, Berlin/Heidelberg, Sept. (2006)Google Scholar
  118. 118.
    van der Aalst, W.M.P., ter Hofstede, A.H.M.: YAWL: yet another workflow language. Inf. Syst. 30(4), 245–275 (2005)CrossRefGoogle Scholar
  119. 119.
    van der Aalst, W.M.P., ter Hofstede, A.H.M., Kiepuszewski, B., Barros, A.P.: Workflow patterns. Distrib. Parallel Databases 14(1), 5–51 (2003)CrossRefGoogle Scholar
  120. 120.
    Vierheller, J.: Exploratory data analysis. In: Process Design for Natural Scientists: An Agile Model-Driven Approach, vol. 500 of CCIS. Springer, Berlin, Heidelberg (2014)Google Scholar
  121. 121.
    von der Beeck, M., Braun, V., Claßen, A., Dannecker, A., Friedrich, C., Koschützki, D., Margaria, T., Schreiber, F., Steffen, B.: Graphs in METAFrame: the unifying power of polymorphism. In: Brinksma, E. (ed.) TACAS, pp. 112–129 (1997)Google Scholar
  122. 122.
    Wassink, I., van der Vet, P.E., Wolstencroft, K., Neerincx, P.B., Roos, M., Rauwerda, H., Breit, T.M.: Analysing scientific workflows: why workflows not only connect web services. In: Services, IEEE Congress on, pp. 314–321 (2009)Google Scholar
  123. 123.
    P. D. W. WebServices. http://wortschatz.uni-leipzig.de/Webservices/. last accessed 15 Jan 2016
  124. 124.
    Wickert, A., Lamprecht, A.-L.: jABCstats: an extensible process library for the empirical analysis of jABC workflows. In: Margaria, T., Steffen, B. (eds.) Leveraging Applications of Formal Methods, Verification and Validation. Specialized Techniques and Applications, vol. 8803 of Lecture Notes in Computer Science, pp. 449–463. Springer, Berlin (2014)Google Scholar
  125. 125.
    Wiechert, W.: 13C metabolic flux analysis. Metab. Eng. 3(3), 195–206 (2001)CrossRefGoogle Scholar
  126. 126.
    Wilkinson, M.D., Links, M.: BioMOBY: an open source biological web services proposal. Brief. Bioinform. 3(4), 331–341 (2002)CrossRefGoogle Scholar
  127. 127.
    Wilkinson, M.D., Vandervalk, B., McCarthy, L.: SADI semantic web services-’cause you can’t always GET what you want! In: Proceedings of the IEEE Services Computing Conference: 7–11 December 2009, Singapore. APSCC 2009, pp. 13–18. IEEE Asia-Pacific (2009)Google Scholar
  128. 128.
    Wilkinson, M.D., Vandervalk, B., McCarthy, L.: The semantic automated discovery and integration (SADI) web service design-pattern, API and reference implementation. J. Biomed. Semant. 2(1), 8 (2011)CrossRefGoogle Scholar
  129. 129.
    Windmüller, S., Neubauer, J., Steffen, B., Howar, F., Bauer, O.: Active continuous quality control. In: 16th international ACM SIGSOFT symposium on component-based software engineering. CBSE ’13, pp. 111–120. ACM SIGSOFT, New York, NY, USA (2013)Google Scholar
  130. 130.
    Wing, J.M.: Computational thinking. Commun. ACM 49(3), 33–35 (2006)MathSciNetCrossRefGoogle Scholar
  131. 131.
    Withers, D., Kawas, E., McCarthy, L., Vandervalk, B., Wilkinson, M.: Semantically-guided workflow construction in Taverna: the SADI and BioMoby plug-ins. In: Margaria, T., Steffen, B. (eds.) 4th International Symposium on Leveraging Applications of Formal Methods. Verification, and Validation (ISoLA 2010)-Vol. Part I, volume 6416 of Lecture Notes in Computer Science, pp. 301–312. Springer, Berlin/Heidelberg (2010)Google Scholar
  132. 132.
    Wolstencroft, K., Haines, R., Fellows, D., Williams, A., Withers, D., Owen, S., Soiland-Reyes, S., Dunlop, I., Nenadic, A., Fisher, P., Bhagat, J., Belhajjame, K., Bacall, F., Hardisty, A.: Nieva de la Hidalga, A., Balcazar Vargas, M.P., Sufi, S., Goble, C.: The Taverna workflow suite: designing and executing workflows of web services on the desktop, web or in the cloud. Nucleic Acids Res. 41(W1), W557–W561 (2013)Google Scholar
  133. 133.
    Wrobel, M., Bisaro, A., Reusser, D., Kropp, J.P.: Novel approaches for web-based access to climate change adaptation information-MEDIATION adaptation platform and ci:grasp-2. In: Hřebíček, J., Schimak, G., Kubásek, M., Rizzoli, A. (eds.) Environmental Software Systems. Fostering Information Sharing, vol. 413 of IFIP Advances in Information and Communication Technology, pp. 489–499. Springer, Berlin (2013)Google Scholar
  134. 134.
    Yu, J., Buyya, R.: A taxonomy of scientific workflow systems for grid computing. SIGMOD Rec. 34(3), 44–49 (2005)CrossRefGoogle Scholar
  135. 135.
    Zamboni, N., Fischer, E., Sauer, U.: FiatFlux-a software for metabolic flux analysis from 13C-glucose experiments. BMC Bioinform. 6, 209 (2005)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Anna-Lena Lamprecht
    • 1
    Email author
  • Bernhard Steffen
    • 2
  • Tiziana Margaria
    • 1
  1. 1.Lero - The Irish Software Research CentreUniversity of LimerickLimerickIreland
  2. 2.Chair of Programming SystemsTU Dortmund UniversityDortmundGermany

Personalised recommendations