Modeling and Execution of Scientific Workflows with the jABC Framework

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.

[1]  Tiziana Margaria,et al.  Service-Oriented Design: The Roots , 2005, ICSOC.

[2]  Sameer Velankar,et al.  SOAP-based services provided by the European Bioinformatics Institute , 2005, Nucleic Acids Res..

[3]  Tiziana Margaria,et al.  MaTRICS: A service-based management tool for remote intelligent configuration of systems , 2006, Innovations in Systems and Software Engineering.

[4]  Tiziana Margaria,et al.  Tool-supported enhancement of diagnosis in model-driven verification , 2009, Innovations in Systems and Software Engineering.

[5]  Tiziana Margaria,et al.  Model-Driven Development with the jABC , 2006, Haifa Verification Conference.

[6]  Sven Jörges,et al.  Construction and Evolution of Code Generators , 2013, Lecture Notes in Computer Science.

[7]  Tiziana Margaria,et al.  Synthesis-Based Loose Programming , 2010, 2010 Seventh International Conference on the Quality of Information and Communications Technology.

[8]  Perdita Stevens,et al.  Modelling Recursive Calls with UML State Diagrams , 2003, FASE.

[9]  Tiziana Margaria,et al.  Bio-jETI: a framework for semantics-based service composition , 2009, BMC Bioinformatics.

[10]  Tiziana Margaria,et al.  Verification, Diagnosis and Adaptation: Tool supported enhancement of the model-driven verification process , 2007, ISoLA.

[11]  Tiziana Margaria,et al.  Incremental Formalization: A Key to Industrial Success , 1996, Softw. Concepts Tools.

[12]  André Platzer,et al.  Correct System Design , 2015, Lecture Notes in Computer Science.

[13]  Anna-Lena Lamprecht,et al.  The Course's SIB Libraries , 2014, Process Design for Natural Scientists.

[14]  Tiziana Margaria,et al.  Design for Verifiability: The OCS Case Study , 2012 .

[15]  Munindar P. Singh,et al.  Service-Oriented Computing: Key Concepts and Principles , 2005, IEEE Internet Comput..

[16]  Rodrigo Lopez,et al.  A new bioinformatics analysis tools framework at EMBL–EBI , 2010, Nucleic Acids Res..

[17]  Bernhard Steffen,et al.  Model-Checking: A Tutorial Introduction , 1999, SAS.

[18]  Tiziana Margaria,et al.  The Electronic Tool Integration platform: concepts and design , 1997, International Journal on Software Tools for Technology Transfer.

[19]  Wil M. P. van der Aalst,et al.  Handbook of Research on Business Process Modeling , 2009 .

[20]  Roy Fielding,et al.  Architectural Styles and the Design of Network-based Software Architectures"; Doctoral dissertation , 2000 .

[21]  João Saraiva,et al.  Generative and Transformational Techniques in Software Engineering II , 2007, Lecture Notes in Computer Science.

[22]  Tiziana Margaria,et al.  Service-Orientation: Conquering Complexity with XMDD , 2012, Conquering Complexity.

[23]  Edmund M. Clarke,et al.  Model Checking , 1999, Handbook of Automated Reasoning.

[24]  Rodrigo Lopez,et al.  Web Services at the European Bioinformatics Institute , 2007, Nucleic Acids Res..

[25]  Tiziana Margaria,et al.  Building Code Generators with Genesys: A Tutorial Introduction , 2009, GTTSE.

[26]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[27]  Bernhard Steffen,et al.  Loose Programming with PROPHETS , 2012, FASE.

[28]  Anna-Lena Lamprecht,et al.  User-Level Workflow Design , 2013, Lecture Notes in Computer Science.

[29]  Tiziana Margaria,et al.  Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes , 2008, BMC Bioinformatics.

[30]  Tiziana Margaria,et al.  Incremental Requirement Specification for Evolving Systems , 2001, Nord. J. Comput..

[31]  Oliver Eulenstein,et al.  Bioinformatics Research and Applications , 2008 .

[32]  Walter H. F. Smith,et al.  Free software helps map and display data , 1991 .

[33]  Tiziana Margaria,et al.  Genesys: service-oriented construction of property conform code generators , 2008, Innovations in Systems and Software Engineering.

[34]  Tiziana Margaria,et al.  Lightweight coarse-grained coordination: a scalable system-level approach , 2004, International Journal on Software Tools for Technology Transfer.

[35]  Tiziana Margaria,et al.  The jABC Approach to Rigorous Collaborative Development of SCM Applications , 2008, ISoLA.

[36]  Tiziana Margaria,et al.  A constraint-based variability modeling framework , 2012, International Journal on Software Tools for Technology Transfer.

[37]  Tiziana Margaria,et al.  Backtracking-Free Design Planning by Automatic Synthesis in METAFrame , 1998, FASE.

[38]  Tiziana Margaria,et al.  jETI: A Tool for Remote Tool Integration , 2005, TACAS.

[39]  Tiziana Margaria,et al.  Customer-Oriented Business Process Management: Vision and Obstacles , 2012, Conquering Complexity.

[40]  Tiziana Margaria,et al.  Process Design for Natural Scientists , 2014, Communications in Computer and Information Science.

[41]  Gerard J. Holzmann,et al.  Conquering Complexity , 2012, Springer London.

[42]  Tiziana Margaria,et al.  High Service Availability in MaTRICS for the OCS , 2008, ISoLA.

[43]  Tiziana Margaria,et al.  Service-oriented Mediation with jABC/jETI , 2009, Semantic Web Services Challenge.

[44]  David M. Booth,et al.  Web Services Architecture , 2004 .

[45]  Rajeev Alur,et al.  A Temporal Logic of Nested Calls and Returns , 2004, TACAS.

[46]  Tiziana Margaria,et al.  Seven Variations of an Alignment Workflow - An Illustration of Agile Process Design and Management in Bio-jETI , 2008, ISBRA.

[47]  Tiziana Margaria,et al.  Community Usage of the Online Conference Service: an Experience Report from three CS Conferences , 2002, I3E.

[48]  Fabio Casati,et al.  Service-Oriented Computing - ICSOC 2005, Third International Conference, Amsterdam, The Netherlands, December 12-15, 2005, Proceedings , 2005, ICSOC.

[49]  Tiziana Margaria,et al.  Service Is in the Eyes of the Beholder , 2007, Computer.

[50]  Tiziana Margaria,et al.  METAFrame in Practice: Design of Intelligent Network Services , 1999, Correct System Design.

[51]  Tiziana Margaria,et al.  Agile IT: Thinking in User-Centric Models , 2008, ISoLA.

[52]  Tiziana Margaria,et al.  Community Usage of the Online Conference Service , 2003 .