@article{OpitzWuennemannAichneretal.2012, author = {Opitz, Stephan and W{\"u}nnemann, Bernd and Aichner, Bernhard and Dietze, Elisabeth and Hartmann, Kai and Herzschuh, Ulrike and IJmker, Janneke and Lehmkuhl, Frank and Li, Shijie and Mischke, Steffen and Plotzki, Anna and Stauch, Georg and Diekmann, Bernhard}, title = {Late Glacial and Holocene development of Lake Donggi Cona, north-eastern Tibetan Plateau, inferred from sedimentological analysis}, series = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences}, volume = {337}, journal = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences}, number = {23}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0031-0182}, doi = {10.1016/j.palaeo.2012.04.013}, pages = {159 -- 176}, year = {2012}, abstract = {Sediments of Lake Donggi Cona on the northeastern Tibetan Plateau were studied to infer changes in the lacustrine depositional environment, related to climatic and non-climatic changes during the last 19 kyr. The lake today fills a 30x8 km big and 95 m deep tectonic basin, associated with the Kunlun Fault. The study was conducted on a sediment-core transect through the lake basin, in order to gain a complete picture of spatio-temporal environmental change. The recovered sediments are partly finely laminated and are composed of calcareous muds with variable amounts of carbonate micrite, organic matter, detrital silt and clay. On the basis of sedimentological, geochemical, and mineralogical data up to five lithological units (LU) can be distinguished that document distinct stages in the development of the lake system. The onset of the lowermost LU with lacustrine muds above basal sands indicates that lake level was at least 39 m below the present level and started to rise after 19 ka, possibly in response to regional deglaciation. At this time, the lacustrine environment was characterized by detrital sediment influx and the deposition of siliciclastic sediment. In two sediment cores, upward grain-size coarsening documents a lake-level fall after 13 cal ka BP, possibly associated with the late-glacial Younger Dryas stadial. From 11.5 to 4.3 cal ka BP, grain-size fining in sediment cores from the profundal coring sites and the onset of lacustrine deposition at a litoral core site (2 m water depth) in a recent marginal bay of Donggi Cona document lake-level rise during the early to mid-Holocene to at least modern level. In addition, high biological productivity and pronounced precipitation of carbonate micrites are consistent with warm and moist climate conditions related to an enhanced influence of summer monsoon. At 4.3 cal ka BP the lake system shifted from an aragonite- to a calcite-dominated system, indicating a change towards a fully open hydrological lake system. The younger clay-rich sediments are moreover non-laminated and lack any diagenetic sulphides, pointing to fully ventilated conditions, and the prevailing absence of lake stratification. This turning point in lake history could imply either a threshold response to insolation-forced climate cooling or a response to a non-climatic trigger, such as an erosional event or a tectonic pulse that induced a strong earthquake, which is difficult to decide from our data base.}, language = {en} } @article{AichnerHerzschuhWilkesetal.2012, author = {Aichner, Bernhard and Herzschuh, Ulrike and Wilkes, Heinz and Schulz, Hans-Martin and Wang, Yongbo and Plessen, Birgit and Mischke, Steffen and Diekmann, Bernhard and Zhang, Chengjun}, title = {Ecological development of Lake Donggi Cona, north-eastern Tibetan Plateau, since the late glacial on basis of organic geochemical proxies and non-pollen palynomorphs}, series = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences}, volume = {313}, journal = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences}, number = {2}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0031-0182}, doi = {10.1016/j.palaeo.2011.10.015}, pages = {140 -- 149}, year = {2012}, abstract = {Organic geochemical proxy data from surface sediment samples and a sediment core from Lake Donggi Cona were used to infer environmental changes on the northeastern Tibetan Plateau spanning the last 18.4 kyr. Long-chain n-alkanes dominate the aliphatic hydrocarbon fraction of the sediment extract from most surface sediment samples and the sediment core. Unsaturated mid-chain n-alkanes (nC(23:1) and nC(25:1)) have high abundances in some samples, especially in core samples from the late glacial and early Holocene. TOC contents, organic biomarker and non-pollen-palynomorph concentrations and results from organic petrologic analysis on selected samples suggest three major episodes in the history of Lake Donggi Cona. Before ca. 12.6 cal ka BP samples contain low amounts of organic matter due to cold and arid conditions during the late glacial. After 12.6 cal ka BP, relatively high contents of TOC and concentrations of Botryococcus fossils, as well as enhanced concentrations of mid-chain n-alkanes and n-alkenes suggest a higher primary and macrophyte productivity than at present This is supported by high contents of palynomorphs derived from higher plants and algae and was possibly triggered by a decrease of salinity and amelioration of climate during the early Holocene. Since 6.8 cal ka BP Lake Donggi Cona has been an oligotrophic freshwater lake. Proxy data suggest that variations in insolation drive ecological changes in the lake, with increased aquatic productivity during the early Holocene summer insolation maximum. Short-term drops of TOC contents or biomarker concentrations (at 9.9 cal ka BP, after 8.0 and between 3.5 and 1.7 cal ka BP) can possibly be related to relatively cool and dry episodes reported from other sites on the north-eastern Tibetan Plateau, which are hypothesized to occur in phase with Northern Hemisphere cooling events.}, language = {en} } @misc{AbramowskiAharonianBenkhalietal.2015, author = {Abramowski, Attila and Aharonian, Felix A. and Benkhali, Faical Ait and Akhperjanian, A. G. and Ang{\"u}ner, Ekrem Oǧuzhan and Backes, Michael and Balenderan, Shangkari and Balzer, Arnim and Barnacka, Anna and Becherini, Yvonne and Tjus, Julia Becker and Berge, David and Bernhard, Sabrina and Bernl{\"o}hr, Konrad and Birsin, E. and Biteau, Jonathan and B{\"o}ttcher, Markus and Boisson, Catherine and Bolmont, J. and Bordas, Pol and Bregeon, Johan and Brun, Francois and Brun, Pierre and Bryan, Mark and Bulik, Tomasz and Carrigan, Svenja and Casanova, Sabrina and Chadwick, Paula M. and Chakraborty, Nachiketa and Chalme-Calvet, R. and Chaves, Ryan C. G. and Chretien, M. and Colafrancesco, Sergio and Cologna, Gabriele and Conrad, Jan and Couturier, Claire and Cui, Yudong and Davids, Isak Delberth and Degrange, Bernhard and Deil, Christoph and deWilt, P. and Djannati-Ata{\"i}, A. and Domainko, Wilfried and Donath, Axel and Dubus, G. and Dutson, K. and Dyks, J. and Dyrda, M. and Edwards, Tanya and Egberts, Kathrin and Eger, Peter and Espigat, P. and Farnier, C. and Fegan, Stephen and Feinstein, Fabrice and Fernandes, Milton Virgilio and Fernandez, Diane and Fiasson, A. and Fontaine, Gerard and F{\"o}rster, Andreas and Fuessling, M. and Gabici, S. and Gajdus, M. and Gallant, Yves A. and Garrigoux, Tania and Giavitto, G. and Giebels, Berrie and Glicenstein, Jean-Francois and Gottschall, Daniel and Grondin, M. -H. and Grudzinska, M. and Hadasch, Daniela and Haeffner, S. and Hahn, Joachim and Harris, Jonathan and Heinzelmann, G{\"o}tz and Henri, G. and Hermann, German and Hervet, O. and Hillert, Andreas and Hinton, James Anthony and Hofmann, Werner and Hofverberg, Petter and Holler, Markus and Horns, Dieter and Ivascenko, Alex and Jacholkowska, A. and Jahn, C. and Jamrozy, Marek and Janiak, M. and Jankowsky, F. and Jung-Richardt, I. and Kastendieck, Max Anton and Katarzynski, K. and Katz, U. and Kaufmann, S. and Khelifi, B. and Kieffer, Michel and Klepser, S. and Klochkov, Dmitry and Kluzniak, W. and Kolitzus, David and Komin, Nu and Kosack, Karl and Krakau, Steffen and Krayzel, F. and Krueger, Pat P. and Laffon, H. and Lamanna, G. and Lefaucheur, J. and Lefranc, Valentin and Lemiere, A. and Lemoine-Goumard, M. and Lenain, J. -P. and Lohse, Thomas and Lopatin, A. and Lu, Chia-Chun and Marandon, Vincent and Marcowith, Alexandre and Marx, Ramin and Maurin, G. and Maxted, Nigel and Mayer, Michael and McComb, T. J. Lowry and Mehault, J. and Meintjes, P. J. and Menzler, Ulf and Meyer, M. and Mitchell, Alison M. W. and Moderski, R. and Mohamed, M. and Mora, K. and Moulin, Emmanuel and Murach, Thomas and de Naurois, Mathieu and Niemiec, J. and Nolan, Sam J. and Oakes, Louise and Odaka, Hirokazu and Ohm, S. and Optiz, Bj{\"o}rn and Ostrowski, Michal and Oya, I. and Panter, Michael and Parsons, R. Daniel and Arribas, M. Paz and Pekeur, Nikki W. and Pelletier, G. and Petrucci, P. -O. and Peyaud, B. and Pita, S. and Poon, Helen and P{\"u}hlhofer, Gerd and Punch, M. and Quirrenbach, A. and Raab, S. and Reichardt, I. and Reimer, Anita and Reimer, Olaf and Renaud, Metz and de los Reyes, Raquel and Rieger, Frank and Romoli, C. and Rosier-Lees, S. and Rowell, G. and Rudak, B. and Rulten, C. B. and Sahakian, Vardan and Salek, D. and Sanchez, David M. and Santangelo, Andrea and Schlickeiser, Reinhard and Schuessler, F. and Schulz, A. and Schwanke, Ullrich and Schwarzburg, S. and Schwemmer, S. and Sol, H. and Spanier, Felix and Spengler, G. and Spies, Franziska and Stawarz, Lukasz and Steenkamp, Riaan and Stegmann, Christian and Stinzing, F. and Stycz, K. and Sushch, Iurii and Tavernet, J. -P. and Tavernier, T. and Taylor, A. M. and Terrier, R. and Tluczykont, Martin and Trichard, C. and Valerius, K. and van Eldik, C. and van Soelen, B. and Vasileiadis, Georges and Veh, J. and Venter, Christo and Viana, Aion and Vincent, P. and Vink, Jacco and V{\"o}lk, Heinrich J. and Volpe, Francesca and Vorster, Martine and Vuillaume, T. and Wagner, S. J. and Wagner, P. and Wagner, R. M. and Ward, Martin and Weidinger, Matthias and Weitzel, Quirin and White, R. and Wierzcholska, A. and Willmann, P. and Woernlein, A. and Wouters, D. and Yang, Ruizhi and Zabalza, Victor and Zaborov, Dmitry and Zacharias, M. and Zdziarski, A. A. and Zech, Alraune and Zechlin, Hannes -S.}, title = {H.E.S.S. detection of TeV emission from the interaction region between the supernova remnant G349.7+0.2 and a molecular cloud (vol 574, A100, 2015)}, series = {Astronomy and astrophysics : an international weekly journal}, volume = {580}, journal = {Astronomy and astrophysics : an international weekly journal}, publisher = {EDP Sciences}, address = {Les Ulis}, organization = {HESS Collaboration}, issn = {1432-0746}, doi = {10.1051/0004-6361/201425070e}, pages = {2}, year = {2015}, language = {en} } @article{MischkeLaiAichneretal.2017, author = {Mischke, Steffen and Lai, Zhongping and Aichner, Bernhard and Heinecke, Liv and Mahmoudov, Zafar and Kuessner, Marie and Herzschuh, Ulrike}, title = {Radiocarbon and optically stimulated luminescence dating of sediments from Lake Karakul, Tajikistan}, series = {Quaternary geochronology : the international research and review journal on advances in quaternary dating techniques}, volume = {41}, journal = {Quaternary geochronology : the international research and review journal on advances in quaternary dating techniques}, publisher = {Elsevier}, address = {Oxford}, issn = {1871-1014}, doi = {10.1016/j.quageo.2017.05.008}, pages = {51 -- 61}, year = {2017}, abstract = {Lake Karakul in the eastern Pamirs is a large and closed-basin lake in a partly glaciated catchment. Two parallel sediment cores were collected from 12 m water depth. The cores were correlated using XRF analysis and dated using radiocarbon and OSL techniques. The age results of the two dating methods are generally in agreement. The correlated composite core of 12.26 m length represents continuous accumulation of sediments in the lake basin since 31 ka. The lake reservoir effect (LRE) remained relatively constant over this period. High sediment accumulation rates (SedARs) were recorded before 23 ka and after 6.5 ka. The relatively close position of the coring location near the eastern shore of the lake implies that high SedARs resulted from low lake levels. Thus, high SedARs and lower lake levels before 23 ka probably reflect cold and dry climate conditions that inhibited the arrival of moist air at high elevation in the eastern Pamirs. Low lake levels after 6.5 ka were probably caused by declining temperatures after the warmer early Holocene, which had caused a reduction in water resources stored as snow, ice and frozen ground in the catchment. Low SedARs during 23-6.5 ka suggest increased lake levels in Lake Karakul. A short-lived increase of SedARs at 15 ka probably corresponds to the rapid melting of glaciers in the Karakul catchment during the Greenland Interstadial le, shortly after glaciers in the catchment had reached their maximum extents. The sediment cores from Lake Karakul represent an important climate archive with robust chronology for the last glacial interglacial cycle from Central Asia. (C) 2017 Elsevier B.V. All rights reserved.}, language = {en} } @article{AichnerMakhmudovRajabovetal.2019, author = {Aichner, Bernhard and Makhmudov, Zafar and Rajabov, Iljomjon and Zhang, Qiong and Pausata, Francesco Salvatore R. and Werner, Martin and Heinecke, Liv and Kuessner, Marie L. and Feakins, Sarah J. and Sachse, Dirk and Mischke, Steffen}, title = {Hydroclimate in the Pamirs Was Driven by Changes in Precipitation-Evaporation Seasonality Since theLast Glacial Period}, series = {Geophysical research letters}, volume = {46}, journal = {Geophysical research letters}, number = {23}, publisher = {American Geophysical Union}, address = {Washington}, issn = {0094-8276}, doi = {10.1029/2019GL085202}, pages = {13972 -- 13983}, year = {2019}, abstract = {The Central Asian Pamir Mountains (Pamirs) are a high-altitude region sensitive to climatic change, with only few paleoclimatic records available. To examine the glacial-interglacial hydrological changes in the region, we analyzed the geochemical parameters of a 31-kyr record from Lake Karakul and performed a set of experiments with climate models to interpret the results. delta D values of terrestrial biomarkers showed insolation-driven trends reflecting major shifts of water vapor sources. For aquatic biomarkers, positive delta D shifts driven by changes in precipitation seasonality were observed at ca. 31-30, 28-26, and 17-14 kyr BP. Multiproxy paleoecological data and modelling results suggest that increased water availability, induced by decreased summer evaporation, triggered higher lake levels during those episodes, possibly synchronous to northern hemispheric rapid climate events. We conclude that seasonal changes in precipitation-evaporation balance significantly influenced the hydrological state of a large waterbody such as Lake Karakul, while annual precipitation amount and inflows remained fairly constant.}, language = {en} } @book{MargariaKubczakSteffen2007, author = {Margaria, Tiziana and Kubczak, Christian and Steffen, Bernhard}, title = {Bio-jETI: a Service Integration, Design, and Provisioning Platform for Orchestrated Bioinformatics Processes - ("part of From Components to Processes")}, series = {Preprint / Universit{\"a}t Potsdam, Institut f{\"u}r Informatik}, volume = {2007, 4}, journal = {Preprint / Universit{\"a}t Potsdam, Institut f{\"u}r Informatik}, publisher = {Univ.}, address = {Potsdam}, issn = {0946-7580}, pages = {16 S.}, year = {2007}, language = {en} } @misc{EbertLamprechtSteffenetal.2012, author = {Ebert, Birgitta E. and Lamprecht, Anna-Lena and Steffen, Bernhard and Blank, Lars M.}, title = {Flux-P}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1054}, issn = {1866-8372}, doi = {10.25932/publishup-47669}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-476696}, pages = {872 -- 890}, year = {2012}, abstract = {Quantitative knowledge of intracellular fluxes in metabolic networks is invaluable for inferring metabolic system behavior and the design principles of biological systems. However, intracellular reaction rates can not often be calculated directly but have to be estimated; for instance, via 13C-based metabolic flux analysis, a model-based interpretation of stable carbon isotope patterns in intermediates of metabolism. Existing software such as FiatFlux, OpenFLUX or 13CFLUX supports experts in this complex analysis, but requires several steps that have to be carried out manually, hence restricting the use of this software for data interpretation to a rather small number of experiments. In this paper, we present Flux-P as an approach to automate and standardize 13C-based metabolic flux analysis, using the Bio-jETI workflow framework. Exemplarily based on the FiatFlux software, it demonstrates how services can be created that carry out the different analysis steps autonomously and how these can subsequently be assembled into software workflows that perform automated, high-throughput intracellular flux analysis of high quality and reproducibility. Besides significant acceleration and standardization of the data analysis, the agile workflow-based realization supports flexible changes of the analysis workflows on the user level, making it easy to perform custom analyses.}, language = {en} } @article{SainiGuentherAichneretal.2017, author = {Saini, Jeetendra and Guenther, Franziska and Aichner, Bernhard and Mischke, Steffen and Herzschuh, Ulrike and Zhang, Chengjun and Maeusbacher, Roland and Gleixner, Gerd}, title = {Climate variability in the past similar to 19,000 yr in NE Tibetan Plateau inferred from biomarker and stable isotope records of Lake Donggi Cona}, series = {Quaternary science reviews : the international multidisciplinary research and review journal}, volume = {157}, journal = {Quaternary science reviews : the international multidisciplinary research and review journal}, publisher = {Elsevier}, address = {Oxford}, issn = {0277-3791}, doi = {10.1016/j.quascirev.2016.12.023}, pages = {129 -- 140}, year = {2017}, abstract = {We investigated 4.84-m-long sediment record spanning over the Late Glacial and Holocene from Lake Donggi Cona to be able to reconstruct circulation pattern on the Tibetan Plateau (TP). Presently, Lake Donggi Cona is located at the boundaries of Westerlies and Asian monsoon circulations in the northeastern TP. However, the exact timing and stimulating mechanisms for climatic changes and monsoon shifts in this region are still debated. We used a 19-ka-long stable isotope record of sedimentary n-alkanes to address this discrepancy by providing insights into paleohydrological conditions. The SD of nC(23) is influenced by lake water evaporation; the BD. values of sedimentary nC(29) are mainly controlled by moisture source and temperature changes. Long-chain n-alkanes dominate over the core whereas three mean clusters (i.e. microbial, aquatic and terrestrial) can be inferred. Multi-proxies suggest five major episodes in the history of Lake Donggi Cona. The Lake Donggi Cona record indicates that the Late Glacial(18.4-14.8 cal ka BP) was dominated by low productivity of mainly microbial and aquatic organisms. Relatively low delta D values suggest low temperatures and moist conditions eventually caused by stronger Westerlies, winter monsoon and melt-water influence. Likely, the shift (similar to 17.9 cal ka BP) from microbial to enhanced aquatic input suggests either a change from deep to shallow water lake or a break in local stratification. Between 14.8 and 13.0 cal ka BP, variable climatic conditions prevailed. Although the Westerlies weekend, the increase in temperature enhanced the permafrost and snow melting (displayed by a high sedimentary accumulation rate). Higher delta D values indicate increasingly arid conditions with higher temperatures which eventually lead to high evaporative conditions and lowest lake levels. Low vegetation cover and high erosion rates led to high sediment accumulation resulting in stratification followed by anoxia in the terminal lake. From 13.0 to 9.2 cal ka BP, lowered values of 813 along with high contents of terrestrial organic matter marked the early-Holocene warming indicating a further strengthening of summer precipitation and higher lake levels. A cooling trend was observed in the mid-Holocene between 9.2 and 3.0 cal ka BP accompanied by higher moisture availability (displayed by lowered SD values) caused by reduced evaporative conditions due to a drop in temperature and recovering Westerlies. After 3.0 cal ka BP, a decrease in lake productivity and cold and semi-arid conditions prevailed suggesting lower lake levels and reduced moisture from recycled air masses and Westerlies. We propose that the summer monsoon was the predominant moisture source during the Belling-Allered warm complex and early -Holocene followed by Westerlies in mid-to-late Holocene period. Stable carbon isotope values-32\%o indicate the absence of C-4 -type vegetation in the region contradicting with their presence in the Lake Qinghai record. The 81) record from lake Donggi Cona highlights the importance of the interplay between Westerlies and summer monsoon circulation at this location, which is highly dynamic in northeastern plateau compared to the North Atlantic circulation and insolation changes. Consequently lake Donggi Cona might be an important anchor point for environmental reconstructions on the Tibetan Plateau. (C) 2017 The Authors. Published by Elsevier Ltd.}, language = {en} } @misc{LamprechtNaujokatMargariaetal.2011, author = {Lamprecht, Anna-Lena and Naujokat, Stefan and Margaria, Tiziana and Steffen, Bernhard}, title = {Semantics-based composition of EMBOSS services}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {956}, issn = {1866-8372}, doi = {10.25932/publishup-43183}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431830}, pages = {23}, year = {2011}, abstract = {Background 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. The Semantic Web, which is meant to address exactly this challenge, is currently one of the most ambitious projects in computer science. Collective efforts within the community have already led to a basis of standards for semantic service descriptions and meta-information. 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. 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. EMBOSS (European Molecular Biology Open Software Suite) is a collection of 350 tools (March 2010) for various sequence analysis tasks, and thus a rich source of services and types that imply comprehensive domain models for planning and synthesis approaches. We use and compare two different setups of our EMBOSS synthesis domain: 1) a manually defined domain setup where an intuitive, high-level, semantically meaningful nomenclature is applied to describe the input/output behavior of the single EMBOSS tools and their classifications, and 2) a domain setup where this information has been automatically derived from the EMBOSS Ajax Command Definition (ACD) files and the EMBRACE Data and Methods ontology (EDAM). Our experiments demonstrate that these domain models in combination with our synthesis methodology greatly simplify working with the large, heterogeneous, and hence manually intractable EMBOSS collection. However, they also show that with the information that can be derived from the (current) ACD files and EDAM ontology alone, some essential connections between services can not be recognized. Conclusions Our results show that adequate domain modeling requires to incorporate as much domain knowledge as possible, far beyond the mere technical aspects of the different types and services. Finding or defining semantically appropriate service and type descriptions is a difficult task, but the bioinformatics community appears to be on the right track towards a Life Science Semantic Web, which will eventually allow automatic service composition methods to unfold their full potential.}, language = {en} } @misc{MargariaKubczakSteffen2008, author = {Margaria, Tiziana and Kubczak, Christian and Steffen, Bernhard}, title = {Bio-jETI}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {822}, doi = {10.25932/publishup-42886}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-428868}, pages = {19}, year = {2008}, abstract = {Background: With Bio-jETI, we introduce a service platform for interdisciplinary work on biological application domains and illustrate its use in a concrete application concerning statistical data processing in R and xcms for an LC/MS analysis of FAAH gene knockout. 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. Conclusions: As a service definition and provisioning platform, Bio-jETI has the potential to become a core technology in interdisciplinary service orchestration and technology transfer. 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 way.}, language = {en} } @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} } @book{LamprechtMagariaSteffenetal.2007, author = {Lamprecht, Anna-Lena and Magaria, Tiziana and Steffen, Bernhard and Sczyrba, Alexander and Hartmeier, Sven and Giegerich, Robert}, title = {GeneFisher-P}, series = {Preprint / Universit{\"a}t Potsdam, Institut f{\"u}r Informatik}, volume = {2007, 3}, journal = {Preprint / Universit{\"a}t Potsdam, Institut f{\"u}r Informatik}, publisher = {Univ.}, address = {Potsdam}, issn = {0946-7580}, pages = {17 S.}, year = {2007}, language = {en} }