@article{KreftingBartBeronovetal.2009, author = {Krefting, Dagmar and Bart, Julian and Beronov, Kamen and Dzhimova, Olga and Falkner, J{\"u}rgen and Hartung, Michael and Hoheisel, Andreas and Knoch, Tobias and Lingner, Thomas and Mohammed, Yassene and Peter, Kathrin and Rahm, Erhard and Sax, Ulrich and Sommerfeld, Dietmar and Steinke, Thomas and Tolxdorff, Thomas and Vossberg, Michael and Viezens, Fred and Weisbecker, Anette}, title = {MediGRID: Towards A User Friendly Secured Grid Infrastructure}, series = {Future Generation Computer Systems (FGCS)}, volume = {25}, journal = {Future Generation Computer Systems (FGCS)}, number = {3}, doi = {10.1016/j.future.2008.05.005}, pages = {281 -- 289}, year = {2009}, language = {en} } @misc{BaumannBuschGottschewskietal., 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}, 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} } @misc{MaySteinke, author = {May, Patrick and Steinke, Thomas}, title = {THESEUS - Protein Structure Prediction at ZIB}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-9184}, number = {06-24}, abstract = {THESEUS, the ZIB threading environment, is a parallel implementation of a protein threading based on a multi-queued branch-and-bound optimal search algorithm to find the best sequence-to-structure alignment through a library of template structures. THESEUS uses a template core model based on secondary structure definition and a scoring function based on knowledge-based potentials reflecting pairwise interactions and the chemical environment, as well as pseudo energies for homology detection, loop alignment, and secondary structure matching. The threading core is implemented in C++ as a SPMD parallization architecture using MPI for communication. The environment is designed for generic testing of different scoring functions, e.g. different secondary structure prediction terms, different scoring matrices and information derived from multiple sequence alignments. A validaton of the structure prediction results has been done on the basis of standard threading benchmark sets. THESEUS successfully participated in the 6th Critical Assessment of Techniques for Protein Structure Prediction (CASP) 2004.}, language = {en} } @misc{StallingSteinke, 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}, 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} } @inproceedings{GesingKacsukKozlovszkyetal.2011, author = {Gesing, Sandra and Kacsuk, Peter and Kozlovszky, Miklos and Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andre and Fels, Gregor and Grunzke, Richard and Herres-Pawlis, Sonja and Kr{\"u}ger, Jens and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Steinke, Thomas and Szikszay Fabri, Anna and Warzecha, Klaus Dieter and Wewior, Martin and Kohlbacher, Oliver}, title = {A Science Gateway for Molecular Simulations}, series = {EGI (European Grid Infrastructure) User Forum 2011, Book of Abstracts}, booktitle = {EGI (European Grid Infrastructure) User Forum 2011, Book of Abstracts}, pages = {94 -- 95}, year = {2011}, language = {en} } @inproceedings{GesingGrunzkeBalaskoetal.2011, author = {Gesing, Sandra and Grunzke, Richard and Balasko, Akos and Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andr{\´e} and Fels, Gregor and Herres-Pawlis, Sonja and Kacsuk, Peter and Kozlovszky, Miklos and Kr{\"u}ger, Jens and Packschies, Lars and Sch{\"a}fer, Patrick and Schuller, Bernd and Schuster, Johannes and Steinke, Thomas and Szikszay Fabri, Anna and Wewior, Martin and M{\"u}ller-Pfefferkorn, Ralph and Kohlbacher, Oliver}, title = {Granular Security for a Science Gateway in Structural Bioinformatics}, series = {Proc. IWSG-Life 2011}, booktitle = {Proc. IWSG-Life 2011}, year = {2011}, language = {en} } @inproceedings{BirkenheuerBlunkBreuersetal.2011, author = {Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andre and Fels, Gregor and Gesing, Sandra and Grunzke, Richard and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kr{\"u}ger, Jens and Lang, Ulrich and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Schuster, Johannes and Steinke, Thomas and Warzecha, Klaus Dieter and Wewior, Martin}, title = {MoSGrid: Progress of Workflow driven Chemical Simulations}, series = {Proc. of Grid Workflow Workshop 2011, Cologne, Germany}, volume = {826}, booktitle = {Proc. of Grid Workflow Workshop 2011, Cologne, Germany}, publisher = {CEUR Workshop Proceedings}, year = {2011}, 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}, series = {6. German Conference on Chemoinformatics}, 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}, series = {6. German Conference on Chemoinformatics}, 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}, series = {Nucleic Acids Res.}, volume = {38}, journal = {Nucleic Acids Res.}, pages = {D326 -- 330}, year = {2010}, language = {en} }