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Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes

Tiziana Margaria, Christian Kubczak, Bernhard Steffen
2008 BMC Bioinformatics  
Methods: Bio-jETI uses the jABC environment for service-oriented modeling and design as a graphical process modeling tool and the jETI service integration technology for remote tool execution.  ...  Domain experts, like biologists not trained in computer science, directly define complex service orchestrations as process models and use efficient and complex bioinformatics tools in a simple and intuitive  ...  , biostatistics and bioinformatics in terms of Life-Science.  ... 
doi:10.1186/1471-2105-9-s4-s12 pmid:18460173 pmcid:PMC2367639 fatcat:y7fq43ei7zdwla3f7cb6xhz3ae

The LearnLib in FMICS-jETI

Tiziana Margaria, Harald Raffelt, Bernhard Steffen, Martin Leucker
2007 12th IEEE International Conference on Engineering Complex Computer Systems (ICECCS 2007)  
, a tool that synthesizes design models by learning from examples, that uses the LearnLib as learner core.  ...  The FMICS-jETI platform is a collaborative, servicebased demonstrator of tools and techniques for the analysis of industrial critical systems.  ...  Choreography jABC originated in the context of the verification of distributed systems [32] , therefore SLGs are inherently adequate as choreography models.  ... 
doi:10.1109/iceccs.2007.43 dblp:conf/iceccs/MargariaRSL07 fatcat:vsyiftdrnrc55n5pvnqfjzl7f4

Scientific Workflows with XMDD: A Way to Use Process Modeling in Computational Science Education

Anna-Lena Lamprecht, Tiziana Margaria
2015 Procedia Computer Science  
In this paper we describe how we apply an XMDD-based process modeling and execution framework for scientific workflow projects in the scope of a computer science course for students with a background in  ...  They can thus play a central role in problem-based computational science education with regard to qualifying students for the design and implementation of software applications for their specific needs  ...  It also shows how to execute and debug jABC process models with the Tracer (the built-in model interpreter) and introduces the idea of the ExecutionContext, a kind of shared memory that jABC process models  ... 
doi:10.1016/j.procs.2015.05.457 fatcat:dczgynl2cbfn5iaec2zoa7s2tu

Continuous Model-Driven Engineering

Tiziana Margaria, Bernhard Steffen
2009 Computer  
Steffen: Business Process Modelling in the jABC: The One-Thing-Approach, Handbook of Research on Business Process Modeling, J. Cardoso and W. van der Aalst (eds.), IGI Global, 2009 [B11] [B11] C.  ...  Margaria: Model Driven Design of Reliable Robot Control Programs Using the jABC Proc.  ... 
doi:10.1109/mc.2009.315 fatcat:glkd4d62u5cy3laikgb3sv5fxa

Bio-jETI: a framework for semantics-based service composition

Anna-Lena Lamprecht, Tiziana Margaria, Bernhard Steffen
2009 BMC Bioinformatics  
The development of bioinformatics databases, algorithms, and tools throughout the last years has lead to a highly distributed world ofbioinformatics services.  ...  Conclusion: We show the power of semantic annotations in an adequately modelled and semantically enabled domain setting.  ...  [7, 28) framework for model-based, graphical design, execution and management of bioinformatics analysis processes.  ... 
doi:10.1186/1471-2105-10-s10-s8 pmid:19796405 pmcid:PMC2755829 fatcat:cxje3kun4banhoocelv6p56uvq

Semantics-based composition of EMBOSS services

Anna-Lena Lamprecht, Stefan Naujokat, Tiziana Margaria, Bernhard Steffen
2011 Journal of Biomedical Semantics  
In combination with process synthesis and planning methods, such knowledge about types and services can facilitate the automatic composition of workflows for particular research questions.  ...  More than in other domains the heterogeneous services world in bioinformatics demands for a methodology to classify and relate resources in a both human and machine accessible manner.  ...  Methods Bio-jETI [17, 30] is a framework for model-based, graphical design, execution and management of bioinformatics analysis processes.  ... 
doi:10.1186/2041-1480-2-s1-s5 pmid:21388574 pmcid:PMC3105497 fatcat:s4m7kglym5gfjd2touwao5goyi

The FMICS-jETI Platform: Status and Perspectives

Tiziana Margaria, Christian Kubczak, Bernhard Steffen, Stefan Naujokat
2006 Second International Symposium on Leveraging Applications of Formal Methods, Verification and Validation (isola 2006)  
We demonstrate here the current status of the FMICS-jETI platform 1 , a collaborative demonstrator based on the jETI technology 2 , that provides as repository a collection of verification tools stemming  ...  One of the goals of FMICS, the ERCIM Working Group on Formal Methods for Industrial Critical Systems (FMICS) [8] , is to transfer and promote the use formal methods technology in industry.  ...  Acknowledgement We thank Ralf Nagel and Stephan Windmüller for their contribution to the jETI environment and to establishing the FMICS-jETI platform.  ... 
doi:10.1109/isola.2006.50 dblp:conf/isola/MargariaKSN06 fatcat:4tqbhvzpirhr3dx7sk2nm23ige

From the How to the What [chapter]

Tiziana Margaria, Bernhard Steffen
2008 Lecture Notes in Computer Science  
In this paper, we consider the Grand Challenge under a very specific perspective: the enabling of application experts without programming knowledge to reliably model their business processes/applications  ...  the application-specific design of platforms tailored for the intended goal.  ...  Application models are the center of the design activity, becoming the first class entities of the global system design process.  ... 
doi:10.1007/978-3-540-69149-5_48 fatcat:rtwnyiskxjf5xei4b7lly6b2yi

Tools and collaborative environments for bioinformatics research

P. Romano, R. Giugno, A. Pulvirenti
2011 Briefings in Bioinformatics  
We also review the principles of Collaborative Development Environments for software and show some examples in Bioinformatics.  ...  In this article, we first present the reasons for an interest of Bioinformatics in this context by also suggesting some research domains that could benefit from collaborative research.  ...  Acknowledgements Authors wish to thank Tom Wiley for his precious support in the preparation of the final version of the article.  ... 
doi:10.1093/bib/bbr055 pmid:21984743 pmcid:PMC3220874 fatcat:nsemkrp6yjgx5biyjwvrlyz534

Web technologies for environmental Big Data

Claudia Vitolo, Yehia Elkhatib, Dominik Reusser, Christopher J.A. Macleod, Wouter Buytaert
2015 Environmental Modelling & Software  
We found that, the processing of the simple datasets used in the pilot proved to be relatively straightforward using a combination of R, RPy2, PyWPS and PostgreSQL.  ...  the design of analysis methods, workflows, and interaction with data sets.  ...  Acknowledgements This work was supported by the Natural Environment Research Council pilot projects on Environmental Virtual Observatory technologies NE/I002200/1 and NE/I004017/1.  ... 
doi:10.1016/j.envsoft.2014.10.007 fatcat:df3mpg7yunaehbfhzysbutze5y

Workflows for quantitative data analysis in the social sciences

Kenneth J. Turner, Paul S. Lambert
2014 International Journal on Software Tools for Technology Transfer (STTT)  
This has motivated the authors to create a more systematic and effective methodology with supporting tools. The approach to modelling quantitative data analysis in the social sciences is presented.  ...  The approach is illustrated with a realistic case study that analyses occupational position in relation to health.  ...  The authors are grateful to their colleagues on DAMES for collaboration on the general topic of techniques for e-social science.  ... 
doi:10.1007/s10009-014-0315-4 fatcat:aw2xfch55ndedos6jwazdc7zxi

The Interoperability Challenge: Building a Model-Driven Digital Thread Platform for CPS [chapter]

Tiziana Margaria, Hafiz Ahmad Awais Chaudhary, Ivan Guevara, Stephen Ryan, Alexander Schieweck
2021 Lecture Notes in Computer Science  
, to the integration of various external databases (for data integration) and to the provision of data analytics capabilities in R.  ...  the individual integrations based on a layered Domain Specific Languages (DSL) approach, 3) through the DSLs it covers the integration space domain by domain, technology by technology, and is thus highly  ...  This work was supported by the Science Foundation Ireland grants 16/RC/3918 (Confirm, the Smart Manufacturing Research Centre) and 13/RC/2094 2 (Lero, the Science Foundation Ireland Research Centre for  ... 
doi:10.1007/978-3-030-89159-6_25 fatcat:prt3qz3qlvavjb3iwkwigkuhm4

Bio-jETI

Tiziana Margaria, Christian Kubczak, Bernhard Steffen
2019
Methods: Bio-jETI uses the jABC environment for service-oriented modeling and design as a graphical process modeling tool and the jETI service integration technology for remote tool execution.  ...  Domain experts, like biologists not trained in computer science, directly define complex service orchestrations as process models and use efficient and complex bioinformatics tools in a simple and intuitive  ...  , biostatistics and bioinformatics in terms of Life-Science.  ... 
doi:10.25932/publishup-42886 fatcat:tnxgvhztsrerbnic2n2dt4mdn4

Improving the Reuse of Services in Geospatial Applications with XMDD Technology

Samih Al-Areqi, Anna-Lena Lamprecht, Tiziana Margaria
2015 The 7th International Conference on Information Technology   unpublished
composition at the user level by using the java application building center (jABC) process modeling framework.  ...  However, due to the specific characteristics of geospatial applications, caused by complex and comprehensive analysis processes and heterogeneous data, the reuse of services faces particular barriers in  ...  This work was supported, in part, by Science Foundation Ireland grant 13/RC/2094 to Lero -the Irish Software Research Centre (www.lero.ie).  ... 
doi:10.15849/icit.2015.0118 fatcat:pgtvvv5plbcptonrl55jirj4ke

Semantics-based composition of EMBOSS services

Anna-Lena Lamprecht, Stefan Naujokat, Tiziana Margaria, Bernhard Steffen
2019
Results In this study we apply the synthesis methodology that is available in the Bio-jETI workflow management framework for the semantics-based composition of EMBOSS services.  ...  More than in other domains the heterogeneous services world in bioinformatics demands for a methodology to classify and relate resources in a both human and machine accessible manner.  ...  Methods Bio-jETI [17, 30] is a framework for model-based, graphical design, execution and management of bioinformatics analysis processes.  ... 
doi:10.25932/publishup-43183 fatcat:u7puungy3bfozjavchlxcgtbaq
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