@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}, 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}, booktitle = {Reconfigurable Systems Summer Institute 2007 (RSSI 2007)}, address = {National Center for Supercomputing Applications, Urbana/Illinois}, year = {2007}, 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.}, 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}, 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}, 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} } @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}, volume = {6}, journal = {BMC Bioinformatics}, doi = {10.1186/1471-2105-6-81}, pages = {81 -- 92}, year = {2005}, language = {en} } @inproceedings{MayKalliesSteinke2005, author = {May, Patrick and Kallies, B. and Steinke, Thomas}, title = {THESEUS - a parallel threading core for highthroughput protein structure prediction}, booktitle = {Proceedings of the 7th Congress of the World Association of Theoretically Orientes Chemists (WARTOC)}, year = {2005}, language = {en} } @inproceedings{MaySteinkeMeyer2004, author = {May, Patrick and Steinke, Thomas and Meyer, Michael}, title = {THESEUS: A Parallel Threading Core}, 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{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}, 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{MayEhrlichSteinke2006, author = {May, Patrick and Ehrlich, Hans-Christian and Steinke, Thomas}, title = {ZIB Structure Prediction Pipeline: Composing a Complex Biological Workflow Through Web Services}, 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{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}, volume = {7}, journal = {BMC Bioinformatics}, pages = {510}, year = {2006}, language = {en} } @inproceedings{SteinkeReinefeld2006, author = {Steinke, Thomas and Reinefeld, Alexander}, title = {Experiences with High-Level Programming of FPGAs on Cray XD1}, booktitle = {CUG Proceedings}, year = {2006}, language = {en} } @article{CordesPreissnerSteinke2003, author = {Cordes, Frank and Preissner, Robert and Steinke, Thomas}, title = {How Does a Protein Work?}, volume = {18}, journal = {BioTOPics J. of Biotechnology Berlin-Brandenburg}, number = {2}, pages = {4 -- 5}, year = {2003}, language = {en} } @article{ZieglerOgurreckSteinkeetal.2010, author = {Ziegler, Alexander and Ogurreck, Malte and Steinke, Thomas and Beckmann, Felix and Prohaska, Steffen and Ziegler, Andreas}, title = {Opportunities and challenges for digital morphology}, volume = {5}, journal = {Biology Direct}, number = {1}, doi = {10.1186/1745-6150-5-45}, pages = {45}, year = {2010}, language = {en} } @inproceedings{WendeNoackSchuettetal.2015, author = {Wende, Florian and Noack, Matthias and Sch{\"u}tt, Thorsten and Sachs, Stephen and Steinke, Thomas}, title = {Application Performance on a Cray XC30 Evaluation System with Xeon Phi Coprocessors at HLRN-III}, booktitle = {Cray User Group}, year = {2015}, language = {en} } @incollection{BaumannLaubenderLaeuteretal.2015, author = {Baumann, Wolfgang and Laubender, Guido and L{\"a}uter, Matthias and Reinefeld, Alexander and Schimmel, Christian and Steinke, Thomas and Tuma, Christian and Wollny, Stefan}, title = {HLRN-III at Zuse Institute Berlin}, booktitle = {Contemporary High Performance Computing: From Petascale toward Exascale, Volume Two}, editor = {Vetter, Jeffrey S.}, publisher = {Chapman and Hall/CRC}, isbn = {9781498700627}, pages = {81 -- 114}, year = {2015}, language = {en} } @inproceedings{WendeCordesSteinke2014, author = {Wende, Florian and Cordes, Frank and Steinke, Thomas}, title = {Concurrent Kernel Execution on Xeon Phi within Parallel Heterogeneous Workloads}, volume = {8632}, booktitle = {Euro-Par 2014: Parallel Processing. 20th International Conference, Porto, Portugal, August 25-29, 2014, Proceedings}, doi = {10.1007/978-3-319-09873-9_66}, pages = {788 -- 799}, year = {2014}, language = {en} } @inproceedings{WendeLaubenderSteinke2014, author = {Wende, Florian and Laubender, Guido and Steinke, Thomas}, title = {Integration of Intel Xeon Phi Servers into the HLRN-III Complex: Experiences, Performance and Lessons Learned}, booktitle = {CUG2014 Proceedings}, year = {2014}, language = {en} } @inproceedings{WendeSteinke2013, author = {Wende, Florian and Steinke, Thomas}, title = {Swendsen-Wang Multi-Cluster Algorithm for the 2D/3D Ising Model on Xeon Phi and GPU}, booktitle = {Proceeding SC '13 Proceedings of SC13: International Conference for High Performance Computing, Networking, Storage and Analysis Article No. 83 ACM New York, NY, USA, 2013}, doi = {http://dx.doi.org/10.1145/2503210.2503254}, year = {2013}, language = {en} } @misc{BenkridElArabyHuangetal.2012, 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}, volume = {2012}, journal = {International Journal of Reconfigurable Computing}, doi = {10.1155/2012/104963}, pages = {1 -- 2}, year = {2012}, language = {en} }