@misc{StallingSteinke1996, author = {Stalling, Detlev and Steinke, Thomas}, title = {Visualization of Vector Fields in Quantum Chemistry}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-2124}, number = {SC-96-01}, year = {1996}, abstract = {\small Many interesting phenomena in molecular systems like interactions between macro-molecules, protein-substrate docking, or channeling processes in membranes are gouverned to a high degree by classical Coulomb or van-der-Waals forces. The visualization of these force fields is important for verifying numerical simulations. Moreover, by inspecting the forces visually we can gain deeper insight into the molecular processes. Up to now the visualization of vector fields is quite unusual in computational chemistry. In fact many commercial software packages do not support this topic at all. The reason is not that vector fields are considered unimportant, but mainly because of the lack of adequate visualization methods. In this paper we survey a number of methods for vector field visualization, ranging from well-known concepts like arrow or streamline plots to more advanced techniques like line integral convolution, and show how these can be applied to computational chemistry. A combination of the most meaningful methods in an interactive 3D visualization environment can provide a powerful tool box for analysing simulations in molecular dynamics.}, language = {en} } @misc{BaumannBuschGottschewskietal.1997, author = {Baumann, Wolfgang and Busch, Hubert and Gottschewski, J{\"u}rgen and Steinke, Thomas and St{\"u}ben, Hinnerk}, title = {Berliner Landesh{\"o}chstleistungsrechner Parallelrechner Cray T3D/T3E: Betrieb, Nutzung, Projekte, Perspektiven f{\"u}r den Ausbau}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-5504}, number = {TR-97-08}, year = {1997}, abstract = {Seit fast drei Jahren betreibt das Konrad-Zuse-Zentrum f{\"u}r Informationstechnik Berlin (ZIB) Parallelrechner der h{\"o}chsten Leistungsklasse im normalen Rechenzentrumsbetrieb. Bereits im Mai 1995 hat das ZIB {\"u}ber seine Erfahrungen mit dem damals leistungsst{\"a}rksten Parallelrechner Deutschlands berichtet. Das Gesamtkonzept des ZIB sieht weiterhin einen H{\"o}chstleistungsrechner als unabdingbaren Bestandteil des High Performance Scientific Computing (HPSC) im ZIB vor. Der vorliegende Bericht beschreibt die aktuelle Konfiguration, Betriebserfahrungen und die Rechnernutzung sowie typische Rechenleistungen, die f{\"u}r einzelne Anwendungsprogramme erzielt wurden. Beschreibungen der Forschungsgebiete mit den Forschungsgruppen, die den Rechner nutzen und die Anforderungen an den Rechnerausbau, die sich aus deren Arbeiten herleiten, beschließen den Bericht.}, language = {de} } @inproceedings{SteinkePeterBorchert2010, author = {Steinke, Thomas and Peter, Kathrin and Borchert, Sebastian}, title = {Efficiency Considerations of Cauchy Reed-Solomon Implementations on Accelerator and Multi-Core Platforms}, booktitle = {Symposium on Application Accelerators in High Performance Computing (SAAHPC)}, address = {Knoxville, USA}, year = {2010}, language = {en} } @misc{BirkenheuerBlunkBreuersetal.2010, author = {Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andr{\´e} and d. Santos Vieira, I. and Fels, Gregor and Gesing, Sandra and Grunzke, Richard and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kruber, Nico and Kr{\"u}ger, Jens and Lang, U. and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Schmalz, Hans-G{\"u}nther and Steinke, Thomas and Warzecha, Klaus Dieter and Wewior, Martin}, title = {MoSGrid - A Molecular Simulation Grid as a new tool in Computational Chemistry, Biology and Material Science}, journal = {6. German Conference on Chemoinformatics}, year = {2010}, language = {en} } @inproceedings{KruegerBirkenheuerBlunketal.2010, author = {Kr{\"u}ger, Jens and Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andr{\´e} and Fels, Gregor and Gesing, Sandra and Grunzke, Richard and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kruber, Nico and Lang, U. and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Schmalz, Hans-G{\"u}nther and Steinke, Thomas and Warzecha, Klaus Dieter and Wewior, Martin}, title = {Molecular Simulation Grid}, booktitle = {6. German Conference on Chemoinformatics}, publisher = {Gesellschaft Deutscher Chemiker (GDCh)}, year = {2010}, language = {en} } @article{MayKreuchwigSteinkeetal.2010, author = {May, Patrick and Kreuchwig, A. and Steinke, Thomas and Koch, Ina}, title = {PTGL: a database for secondary structure-based protein topologies}, volume = {38}, journal = {Nucleic Acids Res.}, pages = {D326 -- 330}, year = {2010}, language = {en} } @inproceedings{DickmannKasparLoehnhardtetal.2009, author = {Dickmann, Frank and Kaspar, Mathias and L{\"o}hnhardt, Benjamin and Kepper, Nick and Viezens, Fred and Hertel, Frank and Lesnussa, Michael and Mohammed, Yassene and Thiel, Andreas and Steinke, Thomas and Bernarding, Johannes and Krefting, Dagmar and Knoch, Tobias and Sax, Ulrich}, title = {Visualization in Health Grid Environments: A Novel Service and Business Approach}, volume = {5745}, booktitle = {GECON}, publisher = {Springer}, doi = {10.1007/978-3-642-03864-8_12}, pages = {150 -- 159}, year = {2009}, language = {en} } @article{BauerRotherMooretal.2009, author = {Bauer, Raphael and Rother, Kristian and Moor, Peter and Reinert, Knut and Steinke, Thomas and Bujnicki, Janusz and Preissner, Robert}, title = {Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors}, volume = {2}, journal = {Algorithms}, number = {2}, doi = {10.3390/a2020692}, pages = {692 -- 709}, year = {2009}, 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}, volume = {4360}, booktitle = {GCCB}, editor = {Dubitzky, W.}, publisher = {Springer}, pages = {19 -- 32}, year = {2007}, language = {en} } @article{MeyerSteinkeSuehnel2007, author = {Meyer, Michael and Steinke, Thomas and S{\"u}hnel, J{\"u}rgen}, title = {Density functional study of isoguanine tetrad and pentad sandwich complexes with alkali metal ions}, volume = {13}, journal = {Journal of Molecular Modeling}, number = {2}, publisher = {Springer Berlin / Heidelberg}, pages = {335 -- 345}, year = {2007}, 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}, 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}, 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} }