@misc{BenkridElArabyHuangetal., author = {Benkrid, Khaled and El-Araby, Esam and Huang, Miaoqing and Sano, Kentaro and Steinke, Thomas}, title = {High-Performance Reconfigurable Computing - editorial for Special Issue of the International Journal of Reconfigurable Computing}, series = {International Journal of Reconfigurable Computing}, volume = {2012}, journal = {International Journal of Reconfigurable Computing}, doi = {10.1155/2012/104963}, pages = {1 -- 2}, language = {en} } @article{KruegerGrunzkeGesingetal., author = {Kr{\"u}ger, Jens and Grunzke, Richard and Gesing, Sandra and Breuers, Sebastian and Brinkmann, Andr{\´e} and de la Garza, Luis and Kohlbacher, Oliver and Kruse, Martin and Nagel, Wolfgang and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Sch{\"a}rfe, Charlotta and Steinke, Thomas and Schlemmer, Tobias and Warzecha, Klaus Dieter and Zink, Andreas and Herres-Pawlis, Sonja}, title = {The MoSGrid Science Gateway - A Complete Solution for Molecular Simulations}, series = {Journal of Chemical Theory and Computation}, volume = {10}, journal = {Journal of Chemical Theory and Computation}, number = {6}, doi = {10.1021/ct500159h}, pages = {2232 -- 2245}, language = {en} } @inproceedings{DresslerSteinke, author = {Dreßler, Sebastian and Steinke, Thomas}, title = {An Automated Approach for Estimating the Memory Footprint of Non-linear Data Objects}, series = {Euro-Par 2013: Parallel Processing Workshops}, volume = {8374}, booktitle = {Euro-Par 2013: Parallel Processing Workshops}, doi = {10.1007/978-3-642-54420-0_25}, pages = {249 -- 258}, language = {en} } @inproceedings{WeinholdLackorzynskiBierbaumetal., author = {Weinhold, Carsten and Lackorzynski, Adam and Bierbaum, Jan and K{\"u}ttler, Martin and Planeta, Maksym and H{\"a}rtig, Hermann and Shiloh, Amnon and Levy, Ely and Ben-Nun, Tal and Barak, Amnon and Steinke, Thomas and Sch{\"u}tt, Thorsten and Fajerski, Jan and Reinefeld, Alexander and Lieber, Matthias and Nagel, Wolfgang}, title = {FFMK: A Fast and Fault-tolerant Microkernel-based System for Exascale Computing}, series = {SPPEXA Symposium 2016}, booktitle = {SPPEXA Symposium 2016}, doi = {10.1007/978-3-319-40528-5_18}, language = {en} } @inproceedings{FajerskiNoackReinefeldetal., author = {Fajerski, J. and Noack, Matthias and Reinefeld, Alexander and Schintke, Florian and Sch{\"u}tt, Thorsten and Steinke, Thomas}, title = {Fast In-Memory Checkpointing with POSIX API for Legacy Exascale-Applications}, series = {SPPEXA Symposium 2016}, booktitle = {SPPEXA Symposium 2016}, doi = {10.1007/978-3-319-40528-5_19}, language = {en} } @article{HeinzeDipankarHenkenetal., author = {Heinze, Rieke and Dipankar, Anurag and Henken, Cintia Carbajal and Moseley, Christopher and Sourdeval, Odran and Tr{\"o}mel, Silke and Xie, Xinxin and Adamidis, Panos and Ament, Felix and Baars, Holger and Barthlott, Christian and Behrendt, Andreas and Blahak, Ulrich and Bley, Sebastian and Brdar, Slavko and Brueck, Matthias and Crewell, Susanne and Deneke, Hartwig and Di Girolamo, Paolo and Evaristo, Raquel and Fischer, J{\"u}rgen and Frank, Christopher and Friederichs, Petra and G{\"o}cke, Tobias and Gorges, Ksenia and Hande, Luke and Hanke, Moritz and Hansen, Akio and Hege, Hans-Christian and Hose, Corinna and Jahns, Thomas and Kalthoff, Norbert and Klocke, Daniel and Kneifel, Stefan and Knippertz, Peter and Kuhn, Alexander and van Laar, Thriza and Macke, Andreas and Maurer, Vera and Mayer, Bernhard and Meyer, Catrin I. and Muppa, Shravan K. and Neggers, Roeland A. J. and Orlandi, Emiliano and Pantillon, Florian and Pospichal, Bernhard and R{\"o}ber, Niklas and Scheck, Leonhard and Seifert, Axel and Seifert, Patric and Senf, Fabian and Siligam, Pavan and Simmer, Clemens and Steinke, Sandra and Stevens, Bjorn and Wapler, Kathrin and Weniger, Michael and Wulfmeyer, Volker and Z{\"a}ngl, G{\"u}nther and Zhang, Dan and Quaas, Johannes}, title = {Large-eddy simulations over Germany using ICON: a comprehensive evaluation}, series = {Quarterly Journal of the Royal Meteorological Society}, volume = {143}, journal = {Quarterly Journal of the Royal Meteorological Society}, number = {702}, doi = {10.1002/qj.2947}, pages = {69 -- 100}, abstract = {Large-eddy simulations (LES) with the new ICOsahedral Non-hydrostatic atmosphere model (ICON) covering Germany are evaluated for four days in spring 2013 using observational data from various sources. Reference simulations with the established Consortium for Small-scale Modelling (COSMO) numerical weather prediction model and further standard LES codes are performed and used as a reference. This comprehensive evaluation approach covers multiple parameters and scales, focusing on boundary-layer variables, clouds and precipitation. The evaluation points to the need to work on parametrizations influencing the surface energy balance, and possibly on ice cloud microphysics. The central purpose for the development and application of ICON in the LES configuration is the use of simulation results to improve the understanding of moist processes, as well as their parametrization in climate models. The evaluation thus aims at building confidence in the model's ability to simulate small- to mesoscale variability in turbulence, clouds and precipitation. The results are encouraging: the high-resolution model matches the observed variability much better at small- to mesoscales than the coarser resolved reference model. In its highest grid resolution, the simulated turbulence profiles are realistic and column water vapour matches the observed temporal variability at short time-scales. Despite being somewhat too large and too frequent, small cumulus clouds are well represented in comparison with satellite data, as is the shape of the cloud size spectrum. Variability of cloud water matches the satellite observations much better in ICON than in the reference model. In this sense, it is concluded that the model is fit for the purpose of using its output for parametrization development, despite the potential to improve further some important aspects of processes that are also parametrized in the high-resolution model.}, language = {en} } @inproceedings{MayKalliesSteinke2005, author = {May, Patrick and Kallies, B. and Steinke, Thomas}, title = {THESEUS - a parallel threading core for highthroughput protein structure prediction}, series = {Proceedings of the 7th Congress of the World Association of Theoretically Orientes Chemists (WARTOC)}, booktitle = {Proceedings of the 7th Congress of the World Association of Theoretically Orientes Chemists (WARTOC)}, year = {2005}, language = {en} } @inproceedings{MayKrauseEhrlichetal.2005, author = {May, Patrick and Krause, F. and Ehrlich, C. and Maaskola, J. and Steinke, Thomas}, title = {ZIB threading pipeline - A webservice-based, distributed structure prediction workflow.}, series = {Proceedings of the German Conference on Bioinformatics (GCB)}, booktitle = {Proceedings of the German Conference on Bioinformatics (GCB)}, pages = {125 -- 126}, year = {2005}, language = {en} } @inproceedings{MichalskyGoedePreissneretal.2004, author = {Michalsky, E. and Goede, A. and Preissner, Robert and May, Patrick and Steinke, Thomas}, title = {A distributed pipeline for structure prediction}, series = {CASP6 Abstract Book, Sixth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy}, booktitle = {CASP6 Abstract Book, Sixth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy}, pages = {112 -- 114}, year = {2004}, language = {en} } @inproceedings{RotherMuellerTrissletal.2004, author = {Rother, Kristian and M{\"u}ller, Heiko and Trißl, Silke and Koch, Ina and Steinke, Thomas and Preissner, Robert and Fr{\"o}mmel, Cornelius and Leser, Ulf}, title = {Columba: Multidimensional Data Integration of Protein Annotations}, series = {Data Integration in the Life Sciences, First International Workshop, DILS 2004, Leipzig, Germany, March 25-26}, volume = {2994}, booktitle = {Data Integration in the Life Sciences, First International Workshop, DILS 2004, Leipzig, Germany, March 25-26}, editor = {Rahm, Erhard}, publisher = {Springer Berlin / Heidelberg}, doi = {10.1007/978-3-540-24745-6_11}, pages = {156 -- 171}, year = {2004}, language = {en} } @inproceedings{MaySteinkeMeyer2004, author = {May, Patrick and Steinke, Thomas and Meyer, Michael}, title = {THESEUS: A Parallel Threading Core}, series = {Procs. 12th Internat. Conf. on Intelligent Systems for Mol. Bio. (ISMB) and 3rd European Conf. on Comp. Bio. (ECCB), Glasgow}, booktitle = {Procs. 12th Internat. Conf. on Intelligent Systems for Mol. Bio. (ISMB) and 3rd European Conf. on Comp. Bio. (ECCB), Glasgow}, pages = {199}, year = {2004}, language = {en} } @inproceedings{MayEhrlichSteinke2006, author = {May, Patrick and Ehrlich, Hans-Christian and Steinke, Thomas}, title = {ZIB Structure Prediction Pipeline: Composing a Complex Biological Workflow Through Web Services}, series = {Euro-Par 2006 Workshops}, volume = {4375}, booktitle = {Euro-Par 2006 Workshops}, editor = {Lehner, Wolfgang and Meyer, Norbert and Streit, Achim and Stewart, Craig}, publisher = {Springer}, pages = {1148 -- 1158}, year = {2006}, language = {en} } @article{TrisslRotherMuelleretal.2005, author = {Trißl, Silke and Rother, Kristian and M{\"u}ller, Heiko and Steinke, Thomas and Koch, Ina and Preissner, Robert and Fr{\"o}mmel, Cornelius and Leser, Ulf}, title = {Columba: an integrated database of proteins, structures, and annotations}, series = {BMC Bioinformatics}, volume = {6}, journal = {BMC Bioinformatics}, doi = {10.1186/1471-2105-6-81}, pages = {81 -- 92}, year = {2005}, language = {en} } @article{KolbeckMaySchmidtGoenneretal.2006, author = {Kolbeck, Bj{\"o}rn and May, Patrick and Schmidt-Goenner, T. and Steinke, Thomas and Knapp, E.}, title = {Connectivity independent protein-structure alignment: a hierarchical approach}, series = {BMC Bioinformatics}, volume = {7}, journal = {BMC Bioinformatics}, pages = {510}, year = {2006}, language = {en} } @inproceedings{KotthaPeterSteinkeetal.2007, author = {Kottha, Samatha and Peter, Kathrin and Steinke, Thomas and Bart, Julian and Falkner, J{\"u}rgen and Weisbecker, Anette and Viezens, Fred and Mohammed, Yassene and Sax, Ulrich and Hoheisel, Andreas and Ernst, Thilo and Sommerfeld, Dietmar and Krefting, Dagmar and Vossberg, Michael}, title = {Medical Image Processing in MediGRID}, series = {German E-Science Conference}, booktitle = {German E-Science Conference}, publisher = {Max Planck Digital Library}, address = {Baden-Baden}, year = {2007}, language = {en} } @inproceedings{StahlbergBabstPopigetal.2007, author = {Stahlberg, Eric and Babst, Michael and Popig, Daryl and Steinke, Thomas}, title = {Molecular Dynamics with FPGAs: A Portable API Molecular Simulations with Hardware Accelerators: A Portable Interface Definition for FPGA Supported Acceleration}, series = {International Supercomputing Conference 2007 (ISC 2007)}, booktitle = {International Supercomputing Conference 2007 (ISC 2007)}, address = {Dresden}, year = {2007}, language = {en} } @inproceedings{StahlbergPopigRyleetal.2007, author = {Stahlberg, Eric and Popig, Daryl and Ryle, Debie and Babst, Michael and Anderson, Mohammed and Steinke, Thomas}, title = {Molecular Simulations with Hardware Accelerators}, series = {Reconfigurable Systems Summer Institute 2007 (RSSI 2007)}, booktitle = {Reconfigurable Systems Summer Institute 2007 (RSSI 2007)}, address = {National Center for Supercomputing Applications, Urbana/Illinois}, year = {2007}, language = {en} } @inproceedings{RotherTrisslMuelleretal.2003, author = {Rother, Kristian and Trissl, S. and M{\"u}ller, H. and May, Patrick and Heek, R. and Preissner, Robert and Steinke, Thomas and Koch, Ina and Leser, Ulf and Fr{\"o}mmel, Cornelius}, title = {Columba - A Database of Annotations of Protein Structure}, series = {ECCB - Proceedings of the European Conference on Computational Biology in conjunction with the French National Conference on Bioinformatics}, booktitle = {ECCB - Proceedings of the European Conference on Computational Biology in conjunction with the French National Conference on Bioinformatics}, editor = {Christophe, C. and Lenhof, H.-P. and Sagot, M.-F.}, pages = {109 -- 110}, year = {2003}, language = {en} } @inproceedings{SteinkeReinefeld2006, author = {Steinke, Thomas and Reinefeld, Alexander}, title = {Experiences with High-Level Programming of FPGAs on Cray XD1}, series = {CUG Proceedings}, booktitle = {CUG Proceedings}, year = {2006}, language = {en} } @inproceedings{MayKlauBaueretal.2007, author = {May, Patrick and Klau, Gunnar and Bauer, Markus and Steinke, Thomas}, title = {Accelerated microRNA-Precursor Detection Using the Smith-Waterman Algorithm on FPGAs}, series = {GCCB}, volume = {4360}, booktitle = {GCCB}, editor = {Dubitzky, W.}, publisher = {Springer}, pages = {19 -- 32}, year = {2007}, language = {en} }