Skip to main content
Fachgebiete
Automobil + Motoren Bauwesen + Immobilien Business IT + Informatik Elektrotechnik + Elektronik Energie + Nachhaltigkeit Finance + Banking Management + Führung Marketing + Vertrieb Maschinenbau + Werkstoffe Versicherung + Risiko
DE
EN
Bücher
Zeitschriften
Themenseiten
Organisationspsychologie Projektmanagement Marketing Smart Manufacturing
Weitere Formate
Podcasts Webinare Technik Webinare Wirtschaft Kongresse Veranstaltungskalender Awards
Jetzt Einzelzugang starten
Zugang für Unternehmen
Referenzkunden
SLX-Digitalkonferenz: Zukunftswerkstatt 2024

Mehr Umsatz mit Top-Kontakten

Am 7. Mai erfahren Sie, wie Vertriebsteams Leadgenerierung, Leadnurturing und Leadstrategien effizient steuern können.
Erweiterte Suche
Anmelden
nach oben
International Journal on Software Tools for Technology Transfer
Erschienen in: International Journal on Software Tools for Technology Transfer 6/2016

01.11.2016 | SW

Scientific workflows with the jABC framework

A review after a decade in the field

verfasst von: Anna-Lena Lamprecht, Bernhard Steffen, Tiziana Margaria

Erschienen in: International Journal on Software Tools for Technology Transfer | Ausgabe 6/2016

Einloggen

Aktivieren Sie unsere intelligente Suche, um passende Fachinhalte oder Patente zu finden.

search-config
loading …

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.
Vorheriger Artikel Scientific workflows for process mining: building blocks, scenarios, and implementation
Nächster Artikel Provably correct control flow graphs from Java bytecode programs with exceptions

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 340 Zeitschriften

aus folgenden Fachgebieten:

  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Versicherung + Risiko




Jetzt Wissensvorsprung sichern!

Jetzt informieren
Fußnoten
1
An orthologous gene is a gene present in two or more species that has evolved from a common ancestor.
 
Literatur
1.
2.
3.
4.
5.
6.
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)
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)
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)CrossRef
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)
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)
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)CrossRef
13.
Barnes, D., Kölling, M.: Objects First with Java: A Practical Introduction Using BlueJ. Pearson Education International, New York (2009)
14.
15.
Beck, K., Andres, C.: Extreme Programming Explained: Embrace Change. Addison-Wesley Professional, Boston (2004)
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.
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)
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)
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)
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)
21.
Borner, J.: A molecular approach to chelicerate phylogeny. Diploma thesis, Universität Hamburg (2010)
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)
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)CrossRefMATH
24.
Clarke, E.M., Grumberg, O., Peled, D.A.: Model Checking. The MIT Press, Cambridge (1999)
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)CrossRef
26.
Curcin, V., Ghanem, M., Guo, Y.: Analysing scientific workflows with computational tree logic. Clust. Comput. 12, 399–419 (2009)CrossRef
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)
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)CrossRef
29.
Ebert, B.E., Lamprecht, A.-L., Steffen, B., Blank, L.M.: Flux-P: automating metabolic flux analysis. Metabolites 2(4), 872–890 (2012)CrossRef
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)CrossRef
31.
Frohme, M.: Agile Domänenmodellierung für prozessgesteuerte Webanwendungen. Bachelor thesis, TU Dortmund (2013)
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)
33.
Ghanem, M., Curcin, V., Wendel, P., Guo, Y.: Building and Using Analytical Workflows in Discovery Net, pp. 119–139. Wiley, New York (2009)
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)
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)
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)
37.
Hagemeier, D.: GeneFisher2-an AJAX based implementation of GeneFisher-P. Bachelor’s thesis, University Bielefeld, Faculty of Technology, Dec. (2006)
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)
39.
Huhns, M.N., Singh, M.P.: Service-oriented computing: key concepts and principles. IEEE Internet Comput. 9, 75–81 (2005)CrossRef
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)
41.
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)
43.
Jarvis, A., Reuter, H., Nelson, A., Guevara, E.: Hole-filled SRTM for the globe Version 4 last accessed 7 Mar 2014 (2008)
44.
Jonsson, B., Margaria, T., Naeser, G., Nyström, J., Steffen, B.: Incremental requirement specification for evolving systems. Nord. J. Comput. 8, 65–87 (2001)MATH
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)
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)CrossRef
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)CrossRef
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)
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)
50.
Kriewald, S.: srtmtools: SRTM tools. R package version 1, 2013–00 (2013)
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)
52.
Kubczak, C., Margaria, T., Steffen, B., Nagel, R.: Service-oriented Mediation with jABC/jETI (2008)
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)
54.
Lamprecht, A.-L.: User-Level Workflow Design-A Bioinformatics Perspective, volume 8311 of Lecture Notes in Computer Science. Springer (2013)
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)
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)
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)
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)
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)
60.
Lamprecht, A.-L., Margaria, T., Steffen, B.: Bio-jETI: a framework for semantics-based service composition. BMC Bioinform. 10(Suppl 10), S8 (2009)CrossRef
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.
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)CrossRef
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)
64.
Lamprecht, A.-L., Naujokat, S., Margaria, T., Steffen, B.: Semantics-based composition of EMBOSS services. J. Biomed. Semant. 2(Suppl 1), S5 (2011)CrossRef
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)
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)
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)
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)CrossRef
69.
Margaria, T.: Service is in the eyes of the beholder. IEEE Computer, Nov. (2007)
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)CrossRef
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)
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)
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)
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)
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)CrossRef
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)
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)
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)
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)
80.
Margaria, T., Steffen, B.: Continuous model-driven engineering. IEEE. Comput. 42(10), 106–109 (2009)
81.
Margaria, T., Steffen, B.: Simplicity as a driver for agile innovation. Computer 43(6), 90–92 (2010)CrossRef
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)CrossRef
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)
84.
Martín-Requena, V., Ríos, J., García, M., Ramírez, S., Trelles, O.: jORCA: easily integrating bioinformatics web services. Bioinformatics 26(4), 553–559 (2010)CrossRef
85.
McCabe, T.J.: A complexity measure. IEEE Trans. Softw. Eng. SE-2(4):308–320, Dec 1976
86.
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)
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)
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)
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)
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)
92.
Neubauer, J.: Higher-order process engineering. Phd thesis, Technische Universität Dortmund (2014)
93.
Neubauer, J.: Higher-order process engineering: The technical background. Technical report, Technische Universität Dortmund, April (2014)
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)
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)
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)CrossRef
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)CrossRef
98.
Qin, J., Fahringer, T.: Scientific Workflows-Programming, Optimization, and Synthesis with ASKALON and AWDL. Springer, Berlin (2012)MATH
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)CrossRef
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)
101.
Schmidt, D.C.: Guest editor’s introduction: model-driven engineering. IEEE Comput. 39(2), 25–31 (2006)CrossRef
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)
103.
Simon, M.: Automatisierte Konstruktion thematischer Karten-Kartentypen, Prozessdefinition und Prozesssteuerung. Master’s thesis., University of Potdam (2014)
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)CrossRef
105.
Ståhl, D., Bosch, J.: Modeling continuous integration practice differences in industry software development. J. Syst. Softw. 87, 48–59 (2014)CrossRef
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)CrossRef
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)
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)CrossRefMATH
109.
Steffen, B., Margaria, T., Braun, V., Kalt, N.: Hierarchical service definition. Annu. Rev. Commun. ACM 51, 847–856 (1997)
110.
Steffen, B., Margaria, T., Claßen, A., Braun, V.: The METAFrame’95 environment. In: CAV, pp. 450–453 (1996)
111.
Steffen, B., Margaria, T., Claßen, A., Braun, V.: Incremental formalization: a key to industrial success. Softw. Concepts Tools 17(2), 78–95 (1996)
112.
Steffen, B., Margaria, T., Freitag, B.: Module configuration by minimal model construction. Technical report, Fakultät für Mathematik und Informatik, Universität Passau (1993)
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)
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)
115.
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)
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)
118.
van der Aalst, W.M.P., ter Hofstede, A.H.M.: YAWL: yet another workflow language. Inf. Syst. 30(4), 245–275 (2005)CrossRef
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)CrossRef
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)
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)
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)
123.
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)
125.
Wiechert, W.: 13C metabolic flux analysis. Metab. Eng. 3(3), 195–206 (2001)CrossRef
126.
Wilkinson, M.D., Links, M.: BioMOBY: an open source biological web services proposal. Brief. Bioinform. 3(4), 331–341 (2002)CrossRef
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)
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)CrossRef
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)
130.
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)
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)
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)
134.
Yu, J., Buyya, R.: A taxonomy of scientific workflow systems for grid computing. SIGMOD Rec. 34(3), 44–49 (2005)CrossRef
135.
Zamboni, N., Fischer, E., Sauer, U.: FiatFlux-a software for metabolic flux analysis from 13C-glucose experiments. BMC Bioinform. 6, 209 (2005)CrossRef
Metadaten
Titel
Scientific workflows with the jABC framework
A review after a decade in the field
verfasst von
Anna-Lena Lamprecht
Bernhard Steffen
Tiziana Margaria
Publikationsdatum
01.11.2016
Verlag
Springer Berlin Heidelberg
Erschienen in
International Journal on Software Tools for Technology Transfer / Ausgabe 6/2016
Print ISSN: 1433-2779
Elektronische ISSN: 1433-2787
DOI
https://doi.org/10.1007/s10009-016-0427-0

Weitere Artikel der Ausgabe 6/2016

International Journal on Software Tools for Technology Transfer 6/2016 Zur Ausgabe

Regular Paper

Provably correct control flow graphs from Java bytecode programs with exceptions

SW

Using registries to integrate bioinformatics tools and services into workbench environments

Introduction

Scientific workflows

Regular Paper

Equivalence class verification of the contract net protocol-extension

SW

A scalable Cloud-based system for data-intensive spatial analysis

SW

Scientific workflows for process mining: building blocks, scenarios, and implementation

Premium Partner

    Bildnachweise