@article{MargariaSteffen2009, author = {Margaria, Tiziana and Steffen, Bernhard}, title = {Continuous model-driven engineering}, issn = {0018-9162}, year = {2009}, abstract = {Agility at the customer, user, and application level will prove key to aligning and linking business and IT}, language = {en} } @article{OpitzRamischMischkeetal.2013, author = {Opitz, Stephan and Ramisch, Arne and Mischke, Steffen and Diekmann, Bernhard}, title = {Holocene lake stages and thermokarst dynamics in a discontinuous permafrost affected region, north-eastern Tibetan Plateau}, series = {Journal of Asian earth sciences}, volume = {76}, journal = {Journal of Asian earth sciences}, number = {17}, publisher = {Elsevier}, address = {Oxford}, issn = {1367-9120}, doi = {10.1016/j.jseaes.2013.08.006}, pages = {85 -- 94}, year = {2013}, abstract = {Sediments of a thermokarst system on the north-eastern Tibetan Plateau were studied to infer changes in the lacustrine depositional environment related to climatic changes since the early Holocene. The thermokarst pond with a length of 360 m is situated in a 14.5 x 6 km tectonically unaffected intermontane basin, which is underlain by discontinuous permafrost. A lake sediment core and bankside lacustrine onshore deposits were analysed. Additionally, fossil lake sediments were investigated, which document a former lake-level high stand. The sediments are mainly composed of marls with variable amounts of silt carbonate micrite, and organic matter. On the basis of sedimentological (grain size data), geochemical (XRF), mineralogical (XRD) and micropaleontological data (ostracods and chironomide assemblages) a reconstruction of a paleolake environment was achieved. Lacustrine sediments with endogenic carbonate precipitation suggest a lacustrine environment since at least 19.0 cal ka BP. However, because of relocation and reworking processes in the lake, the sediments did not provide distinct information about the ultimate formation of the lake. The high amount of endogenic carbonate suggests prolonged still-water conditions at about 9.3 cal ka BP. Ostracod shells and chironomid head capsules in fossil lake sediments indicate at least one former lake-level high stand, which were developed between the early and middle Holocene. From the late Holocene the area was possibly characterized by a lake-level decline, documented by a hiatus between lacustrine sediments and a reworked loess or loess-like horizon. After the lake-level decline and the following warming period, the area was affected by thermally-induced subsidence and a re-flooding of the basin because of thawing permafrost.}, language = {en} } @article{WangHerzschuhShumilovskikhetal.2014, author = {Wang, Y. and Herzschuh, Ulrike and Shumilovskikh, L. S. and Mischke, Steffen and Birks, H. John B. and Wischnewski, J. and B{\"o}hner, J{\"u}rgen and Schluetz, F. and Lehmkuhl, F. and Diekmann, Bernhard and Wuennemann, B. and Zhang, C.}, title = {Open Access Quantitative reconstruction of precipitation changes on the NE Tibetan Plateau since the Last Glacial Maximum - extending the concept of pollen source area to pollen-based climate reconstructions from large lakes}, series = {Climate of the past : an interactive open access journal of the European Geosciences Union}, volume = {10}, journal = {Climate of the past : an interactive open access journal of the European Geosciences Union}, number = {1}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1814-9324}, doi = {10.5194/cp-10-21-2014}, pages = {21 -- 39}, year = {2014}, abstract = {Pollen records from large lakes have been used for quantitative palaeoclimate reconstruction, but the influences that lake size (as a result of species-specific variations in pollen dispersal patterns that smaller pollen grains are more easily transported to lake centre) and taphonomy have on these climatic signals have not previously been systematically investigated. We introduce the concept of pollen source area to pollen-based climate calibration using the north-eastern Tibetan Plateau as our study area. We present a pollen data set collected from large lakes in the arid to semi-arid region of central Asia. The influences that lake size and the inferred pollen source areas have on pollen compositions have been investigated through comparisons with pollen assemblages in neighbouring lakes of various sizes. Modern pollen samples collected from different parts of Lake Donggi Cona (in the north-eastern part of the Tibetan Plateau) reveal variations in pollen assemblages within this large lake, which are interpreted in terms of the species-specific dispersal and depositional patterns for different types of pollen, and in terms of fluvial input components. We have estimated the pollen source area for each lake individually and used this information to infer modern climate data with which to then develop a modern calibration data set, using both the multivariate regression tree (MRT) and weighted-averaging partial least squares (WA-PLS) approaches. Fossil pollen data from Lake Donggi Cona have been used to reconstruct the climate history of the north-eastern part of the Tibetan Plateau since the Last Glacial Maximum (LGM). The meanannual precipitation was quantitatively reconstructed using WA-PLS: extremely dry conditions are found to have dominated the LGM, with annual precipitation of around 100 mm, which is only 32\% of present-day precipitation. A gradually increasing trend in moisture conditions during the Late Glacial is terminated by an abrupt reversion to a dry phase that lasts for about 1000 yr and coincides with "Heinrich event 1" in the North Atlantic region. Subsequent periods corresponding to the Bolling/Allerod interstadial, with annual precipitation (P-ann) of about 350 mm, and the Younger Dryas event (about 270 mm P-ann) are followed by moist conditions in the early Holocene, with annual precipitation of up to 400 mm. A drier trend after 9 cal. ka BP is followed by a second wet phase in the middle Holocene, lasting until 4.5 cal. ka BP. Relatively steady conditions with only slight fluctuations then dominate the late Holocene, resulting in the present climatic conditions. The climate changes since the LGM have been primarily driven by deglaciation and fluctuations in the intensity of the Asian summer monsoon that resulted from changes in the Northern Hemisphere summer solar insolation, as well as from changes in the North Atlantic climate through variations in the circulation patterns and intensity of the westerlies.}, language = {en} } @article{JoergesMargariaSteffen2011, author = {J{\"o}rges, Sven and Margaria, Tiziana and Steffen, Bernhard}, title = {Assuring property conformance of code generators via model checking}, series = {Formal aspects of computing : the international journal of formal methods}, volume = {23}, journal = {Formal aspects of computing : the international journal of formal methods}, number = {5}, publisher = {Springer}, address = {New York}, issn = {0934-5043}, doi = {10.1007/s00165-010-0169-9}, pages = {589 -- 606}, year = {2011}, abstract = {Automatic code generation is an essential cornerstone of today's model-driven approaches to software engineering. Thus a key requirement for the success of this technique is the reliability and correctness of code generators. This article describes how we employ standard model checking-based verification to check that code generator models developed within our code generation framework Genesys conform to (temporal) properties. Genesys is a graphical framework for the high-level construction of code generators on the basis of an extensible library of well-defined building blocks along the lines of the Extreme Model-Driven Development paradigm. We will illustrate our verification approach by examining complex constraints for code generators, which even span entire model hierarchies. We also show how this leads to a knowledge base of rules for code generators, which we constantly extend by e.g. combining constraints to bigger constraints, or by deriving common patterns from structurally similar constraints. In our experience, the development of code generators with Genesys boils down to re-instantiating patterns or slightly modifying the graphical process model, activities which are strongly supported by verification facilities presented in this article.}, language = {en} } @article{BakeraMargariaRenneretal.2011, author = {Bakera, Marco and Margaria, Tiziana and Renner, Clemens D. and Steffen, Bernhard}, title = {Game-Based model checking for reliable autonomy in space}, series = {Journal of aerospace computing, information, and communication}, volume = {8}, journal = {Journal of aerospace computing, information, and communication}, number = {4}, publisher = {American Institute of Aeronautics and Astronautics}, address = {Reston}, issn = {1940-3151}, doi = {10.2514/1.32013}, pages = {100 -- 114}, year = {2011}, abstract = {Autonomy is an emerging paradigm for the design and implementation of managed services and systems. Self-managed aspects frequently concern the communication of systems with their environment. Self-management subsystems are critical, they should thus be designed and implemented as high-assurance components. Here, we propose to use GEAR, a game-based model checker for the full modal mu-calculus, and derived, more user-oriented logics, as a user friendly tool that can offer automatic proofs of critical properties of such systems. Designers and engineers can interactively investigate automatically generated winning strategies resulting from the games, this way exploring the connection between the property, the system, and the proof. The benefits of the approach are illustrated on a case study that concerns the ExoMars Rover.}, language = {en} } @misc{MargariaSteffenKubczak2010, author = {Margaria, Tiziana and Steffen, Bernhard and Kubczak, Christian}, title = {Evolution support in heterogeneous service-oriented landscapes}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {918}, issn = {1866-8372}, doi = {10.25932/publishup-43240}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-432405}, pages = {15}, year = {2010}, abstract = {We present an approach that provides automatic or semi-automatic support for evolution and change management in heterogeneous legacy landscapes where (1) legacy heterogeneous, possibly distributed platforms are integrated in a service oriented fashion, (2) the coordination of functionality is provided at the service level, through orchestration, (3) compliance and correctness are provided through policies and business rules, (4) evolution and correctness-by-design are supported by the eXtreme Model Driven Development paradigm (XMDD) offered by the jABC (Margaria and Steffen in Annu. Rev. Commun. 57, 2004)—the model-driven service oriented development platform we use here for integration, design, evolution, and governance. The artifacts are here semantically enriched, so that automatic synthesis plugins can field the vision of Enterprise Physics: knowledge driven business process development for the end user. We demonstrate this vision along a concrete case study that became over the past three years a benchmark for Semantic Web Service discovery and mediation. We enhance the Mediation Scenario of the Semantic Web Service Challenge along the 2 central evolution paradigms that occur in practice: (a) Platform migration: platform substitution of a legacy system by an ERP system and (b) Backend extension: extension of the legacy Customer Relationship Management (CRM) and Order Management System (OMS) backends via an additional ERP layer.}, language = {en} } @misc{LamprechtMargariaSteffen2009, author = {Lamprecht, Anna-Lena and Margaria, Tiziana and Steffen, Bernhard}, title = {Bio-jETI : a framework for semantics-based service composition}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45066}, year = {2009}, abstract = {Background: The development of bioinformatics databases, algorithms, and tools throughout the last years has lead to a highly distributedworld of bioinformatics services. Without adequatemanagement and development support, in silico researchers are hardly able to exploit the potential of building complex, specialized analysis processes from these services. The Semantic Web aims at thoroughly equipping individual data and services with machine-processable meta-information, while workflow systems support the construction of service compositions. However, even in this combination, in silico researchers currently would have to deal manually with the service interfaces, the adequacy of the semantic annotations, type incompatibilities, and the consistency of service compositions. Results: In this paper, we demonstrate by means of two examples how Semantic Web technology together with an adequate domain modelling frees in silico researchers from dealing with interfaces, types, and inconsistencies. In Bio-jETI, bioinformatics services can be graphically combined to complex services without worrying about details of their interfaces or about type mismatches of the composition. These issues are taken care of at the semantic level by Bio-jETI's model checking and synthesis features. Whenever possible, they automatically resolve type mismatches in the considered service setting. Otherwise, they graphically indicate impossible/incorrect service combinations. In the latter case, the workflow developermay either modify his service composition using semantically similar services, or ask for help in developing the missing mediator that correctly bridges the detected type gap. Newly developed mediators should then be adequately annotated semantically, and added to the service library for later reuse in similar situations. Conclusion: We show the power of semantic annotations in an adequately modelled and semantically enabled domain setting. Using model checking and synthesis methods, users may orchestrate complex processes from a wealth of heterogeneous services without worrying about interfaces and (type) consistency. The success of this method strongly depends on a careful semantic annotation of the provided services and on its consequent exploitation for analysis, validation, and synthesis. We are convinced that these annotations will become standard, as they will become preconditions for the success and widespread use of (preferred) services in the Semantic Web}, language = {en} } @article{LamprechtMargariaSteffen2014, author = {Lamprecht, Anna-Lena and Margaria, Tiziana and Steffen, Bernhard}, title = {Modeling and Execution of Scientific Workflows with the jABC Framework}, series = {Process Design for Natural Scientists: an agile model-driven approach}, journal = {Process Design for Natural Scientists: an agile model-driven approach}, number = {500}, editor = {Lambrecht, Anna-Lena and Margaria, Tiziana}, publisher = {Springer Verlag}, address = {Berlin}, isbn = {978-3-662-45005-5}, issn = {1865-0929}, pages = {14 -- 29}, year = {2014}, 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.}, language = {en} } @misc{LamprechtMargariaSteffenetal.2008, author = {Lamprecht, Anna-Lena and Margaria, Tiziana and Steffen, Bernhard and Sczyrba, Alexander and Hartmeier, Sven and Giegerich, Robert}, title = {GeneFisher-P}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {868}, issn = {1866-8372}, doi = {10.25932/publishup-43424}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-434241}, pages = {17}, year = {2008}, abstract = {Background: PCR primer design is an everyday, but not trivial task requiring state-of-the-art software. We describe the popular tool GeneFisher and explain its recent restructuring using workflow techniques. We apply a service-oriented approach to model and implement GeneFisher-P, a process-based version of the GeneFisher web application, as a part of the Bio-jETI platform for service modeling and execution. We show how to introduce a flexible process layer to meet the growing demand for improved user-friendliness and flexibility. Results: Within Bio-jETI, we model the process using the jABC framework, a mature model-driven, service-oriented process definition platform. We encapsulate remote legacy tools and integrate web services using jETI, an extension of the jABC for seamless integration of remote resources as basic services, ready to be used in the process. Some of the basic services used by GeneFisher are in fact already provided as individual web services at BiBiServ and can be directly accessed. Others are legacy programs, and are made available to Bio-jETI via the jETI technology. The full power of service-based process orientation is required when more bioinformatics tools, available as web services or via jETI, lead to easy extensions or variations of the basic process. This concerns for instance variations of data retrieval or alignment tools as provided by the European Bioinformatics Institute (EBI). Conclusions: The resulting service-and process-oriented GeneFisher-P demonstrates how basic services from heterogeneous sources can be easily orchestrated in the Bio-jETI platform and lead to a flexible family of specialized processes tailored to specific tasks.}, language = {en} } @article{NaujokatNeubauerLamprechtetal.2014, author = {Naujokat, Stefan and Neubauer, Johannes and Lamprecht, Anna-Lena and Steffen, Bernhard and Joerges, Sven and Margaria, Tiziana}, title = {Simplicity-first model-based plug-in development}, series = {Software : practice \& experience}, volume = {44}, journal = {Software : practice \& experience}, number = {3}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0038-0644}, doi = {10.1002/spe.2243}, pages = {277 -- 297}, year = {2014}, abstract = {In this article, we present our experience with over a decade of strict simplicity orientation in the development and evolution of plug-ins. The point of our approach is to enable our graphical modeling framework jABC to capture plug-in development in a domain-specific setting. The typically quite tedious and technical plug-in development is shifted this way from a programming task to the modeling level, where it can be mastered also by application experts without programming expertise. We show how the classical plug-in development profits from a systematic domain-specific API design and how the level of abstraction achieved this way can be further enhanced by defining adequate building blocks for high-level plug-in modeling. As the resulting plug-in models can be compiled and deployed automatically, our approach decomposes plug-in development into three phases where only the realization phase requires plug-in-specific effort. By using our modeling framework jABC, this effort boils down to graphical, tool-supported process modeling. Furthermore, we support the automatic completion of process sketches for executability. All this will be illustrated along the most recent plug-in-based evolution of the jABC framework, which witnessed quite some bootstrapping effects.}, language = {en} }