Abstract
We summarize here the main characteristics and features of the jABC framework, used in the case studies as a graphical tool for modeling scientific processes and workflows. As a comprehensive environment for service-oriented modeling and design according to the XMDD (eXtreme Model-Driven Design) paradigm, the jABC offers much more than the pure modeling capability. Associated technologies and plugins provide in fact means for a rich variety of supporting functionality, such as remote service integration, taxonomical service classification, model execution, model verification, model synthesis, and model compilation. We describe here in short both the essential jABC features and the service integration philosophy followed in the environment. In our work over the last years we have seen that this kind of service definition and provisioning platform has the potential to become a core technology in interdisciplinary service orchestration and technology transfer: Domain experts, like scientists not specially trained in computer science, directly define complex service orchestrations as process models and use efficient and complex domain-specific tools in a simple and intuitive way.
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References
CSISS/GMU Geospatial Web Services, http://geobrain.laits.gmu.edu/grassweb/manuals/index.html (last accessed September 9, 2013)
Free opensource geocoder and webservices for geonames and openstreetmap data, http://www.gisgraphy.com/ (last accessed September 9, 2013)
geoPlugin to geolocate your visitors, http://www.geoplugin.com/ (last accessed September 9, 2013)
Bajohr, M., Margaria, T.: MaTRICS: A Service-Based Management Tool for Remote Intelligent Configuration of Systems. Innovations in Systems and Software Engineering (ISSE) 2(2), 99–111 (2005)
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. CCIS, vol. 17, pp. 572–586. Springer, Heidelberg (2008)
Bakera, M., Margaria, T., Renner, C., Steffen, B.: Verification, Diagnosis and Adaptation: Tool-supported enhancement of the model-driven verification process. In: Revue des Nouvelles Technologies de l’Information (RNTI-SM-1), pp. 85–98 (December 2007)
Bakera, M., Margaria, T., Renner, C., Steffen, B.: Tool-supported enhancement of diagnosis in model-driven verification. Innovations in Systems and Software Engineering 5, 211–228 (2009)
Booth, D., Haas, H., McCabe, F., Newcomer, E., Champion, M., Ferris, C., Orchard, D.: Web Services Architecture. W3C Working Group Note (February 2004), http://www.w3.org/TR/ws-arch/ (last accessed May 5, 2013)
Clarke, E.M., Grumberg, O., Peled, D.A.: Model Checking. The MIT Press, Cambridge (1999)
Fielding, R.T.: Architectural Styles and the Design of Network-based Software Architectures. PhD thesis, University of California, Irvine (2000)
Finn, R.D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J.E., Gavin, O.L., Gunasekaran, P., Ceric, G., Forslund, K., Holm, L., Sonnhammer, E.L.L., Eddy, S.R., Bateman, A.: The Pfam protein families database. Nucleic Acids Research 38(suppl 1), D211–D222 (2010)
Goujon, M., McWilliam, H., Li, W., Valentin, F., Squizzato, S., Paern, J., Lopez, R.: A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Research 38(Web Server issue), W695–W699 (2010)
Huhns, M.N., Singh, M.P.: Service-Oriented Computing: Key Concepts and Principles. IEEE Internet Computing 9, 75–81 (2005)
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. CCIS, vol. 17, pp. 724–737. Springer, Heidelberg (2008)
Jonsson, B., Margaria, T., Naeser, G., Nyström, J., Steffen, B.: Incremental requirement specification for evolving systems. Nordic J. of Computing 8, 65–87 (2001)
Jörges, S.: Construction and Evolution of Code Generators. LNCS, vol. 7747. Springer, Heidelberg (2013)
Jörges, S., Lamprecht, A.-L., Margaria, T., Schaefer, I., Steffen, B.: A Constraint-based Variability Modeling Framework. International Journal on Software Tools for Technology Transfer (STTT) 14(5), 511–530 (2012)
Jörges, S., Margaria, T., Steffen, B.: Genesys: service-oriented construction of property conform code generators. Innovations in Systems and Software Engineering 4(4), 361–384 (2008)
Jörges, S., Steffen, B., Margaria, T.: Building code generators with genesys: A tutorial introduction. In: Fernandes, J.M., Lämmel, R., Visser, J., Saraiva, J. (eds.) Generative and Transformational Techniques in Software Engineering III. LNCS, vol. 6491, pp. 364–385. Springer, Heidelberg (2011)
Kubczak, C., Margaria, T., Steffen, B., Nagel, R.: Service-oriented Mediation with jABC/jETI (2008)
Labarga, A., Valentin, F., Anderson, M., Lopez, R.: Web services at the European bioinformatics institute. Nucleic Acids Research 35(Web Server issue), W6–W11 (2007)
Lamprecht, A.: Orchestration of Heterogeneous Bioinformatics Processes in Bio-jETI as a Service Integration, Design, and Provisioning Platform. Master’s thesis, Georg-August-Universität Göttingen (August 2007)
Lamprecht, A.-L.: User-Level Workflow Design. LNCS, vol. 8311. Springer, Heidelberg (2013)
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: Măndoiu, I., Wang, S.-L., Zelikovsky, A. (eds.) ISBRA 2008. LNCS (LNBI), vol. 4983, pp. 445–456. Springer, Heidelberg (2008)
Lamprecht, A.-L., Margaria, T., Steffen, B.: Bio-jETI: a framework for semantics-based service composition. BMC Bioinformatics 10(Suppl 10), S8 (2009)
Lamprecht, A.-L., Naujokat, S., Margaria, T., Steffen, B.: Synthesis-Based Loose Programming. In: Proc. of the 7th Int. Conf. on the Quality of Information and Communications Technology (QUATIC 2010), Porto, Portugal, pp. 262–267 (September 2010)
Lamprecht, A.-L., Wickert, A.: The Course’s SIB Libraries. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 30–44. Springer, Heidelberg (2014)
Margaria, T.: Service is in the Eyes of the Beholder. IEEE Computer (November 2007)
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)
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, Deventer, The Netherlands, pp. 497–511. Kluwer, B.V (2002)
Margaria, T., Kubczak, C., Steffen, B.: Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes. BMC Bioinformatics 9(Suppl 4), S12 (2008)
Margaria, T., Nagel, R., Steffen, B.: jETI: A tool for remote tool integration. In: Halbwachs, N., Zuck, L.D. (eds.) TACAS 2005. LNCS, vol. 3440, pp. 557–562. Springer, Heidelberg (2005)
Margaria, T., Steffen, B.: Backtracking-free design planning by automatic synthesis in METAFrame. In: Astesiano, E. (ed.) ETAPS 1998 and FASE 1998. LNCS, vol. 1382, pp. 188–204. Springer, Heidelberg (1998)
Margaria, T., Steffen, B.: Lightweight coarse-grained coordination: a scalable system-level approach. Software Tools for Technology Transfer 5(2-3), 107–123 (2004)
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. CCIS, vol. 17, pp. 490–502. Springer, Berlin (2009)
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 (2009)
Margaria, T., Steffen, B.: Service-Orientation: Conquering Complexity with XMDD. In: Hinchey, M., Coyle, L. (eds.) Conquering Complexity, pp. 217–236. Springer, London (2012)
Margaria, T., Steffen, B., Reitenspieß, M.: Service-oriented design: The roots. In: Benatallah, B., Casati, F., Traverso, P. (eds.) ICSOC 2005. LNCS, vol. 3826, pp. 450–464. Springer, Heidelberg (2005)
Müller-Olm, M., Schmidt, D., Steffen, B.: Model-Checking - A Tutorial Introduction. In: Proceedings of the 6th International Symposium on Static Analysis (SAS 1999), pp. 330–354 (1999)
Naujokat, S., Lamprecht, A.-L., Steffen, B.: Loose programming with PROPHETS. In: de Lara, J., Zisman, A. (eds.) Fundamental Approaches to Software Engineering. LNCS, vol. 7212, pp. 94–98. Springer, Heidelberg (2012)
Neubauer, J., Margaria, T., Steffen, B.: Design for Verifiability: The OCS Case Study. In: Formal Methods for Industrial Critical Systems: A Survey of Applications, ch. 8, pp. 153–178. Wiley-IEEE Computer Society Press (March 2013)
Pillai, S., Silventoinen, V., Kallio, K., Senger, M., Sobhany, S., Tate, J., Velankar, S., Golovin, A., Henrick, K., Rice, P., Stoehr, P., Lopez, R.: SOAP-based services provided by the European Bioinformatics Institute. Nucleic Acids Research 33(Web Server issue), W25–W28 (2005)
Steffen, B., Margaria, T.: METAFrame in practice: Design of intelligent network services. In: Olderog, E.-R., Steffen, B. (eds.) Correct System Design. LNCS, vol. 1710, pp. 390–415. Springer, Heidelberg (1999)
Steffen, B., Margaria, T., Braun, V.: The Electronic Tool Integration platform: concepts and design. International Journal on Software Tools for Technology Transfer (STTT) 1(1-2), 9–30 (1997)
Steffen, B., Margaria, T., Braun, V., Kalt, N.: Hierarchical Service Definition. Annual Review of Communications of the ACM 51, 847–856 (1997)
Steffen, B., Margaria, T., Claßen, A., Braun, V.: Incremental Formalization: A Key to Industrial Success. Software - Concepts and Tools 17(2), 78–95 (1996)
Steffen, B., Margaria, T., Freitag, B.: Module Configuration by Minimal Model Construction. Technical report, Fakultät für Mathematik und Informatik, Universität Passau (1993)
Steffen, B., Margaria, T., Nagel, R., Jörges, S., Kubczak, C.: Model-driven development with the jABC. In: Bin, E., Ziv, A., Ur, S. (eds.) HVC 2006. LNCS, vol. 4383, pp. 92–108. Springer, Heidelberg (2007)
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 1997 (1997)
Wessel, P.: The GMT Home Page, http://gmt.soest.hawaii.edu (last accessed January 3, 2013)
Wessel, P., Smith, W.H.F.: Free software helps map and display data. EOS Trans. Amer. Geophys. U. 72(41) (1991)
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Lamprecht, AL., Margaria, T., Steffen, B. (2014). Modeling and Execution of Scientific Workflows with the jABC Framework. In: Lamprecht, AL., Margaria, T. (eds) Process Design for Natural Scientists. Communications in Computer and Information Science, vol 500. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-45006-2_2
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