@inproceedings{GranzerBreitlingBraunetal.2007, author = {Granzer, Thomas and Breitling, Frank and Braun, Michael and Enke, Harry and R{\"o}blitz, Thomas}, title = {Providing Remote Access to Robotic Telescopes by Adopting Grid Technology}, series = {German e-Science Conference}, booktitle = {German e-Science Conference}, publisher = {Max Planck Digital Library}, year = {2007}, language = {en} } @inproceedings{EnkeSteinmetzRadkeetal.2007, author = {Enke, Harry and Steinmetz, Matthias and Radke, Thomas and Reiser, Angelika and R{\"o}blitz, Thomas and H{\"o}gqvist, Mikael}, title = {AstroGrid-D: Enhancing Astronomic Science with Grid Technology}, series = {German e-Science Conference}, booktitle = {German e-Science Conference}, publisher = {Max Planck Digital Library}, year = {2007}, language = {en} } @phdthesis{Roeblitz, author = {R{\"o}blitz, Thomas}, title = {Co-Reservation of Resources in the Grid}, isbn = {978-3-86853-137-4}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-11626}, abstract = {Executing applications in the Grid often requires access to multiple geographically distributed resources. In a Grid environment, these resources belong to different administrative domains, each employing its own scheduling policy. That is, at which time an activity (e.g., compute job, data transfer) is started, is decided by the resource's local management system. In such an environment, the coordinated execution of distributed applications requires guarantees on the quality of service (QoS) of the needed resources. Reserving resources in advance is an accepted means to obtain QoS guarantees from a single provider. The challenge, however, is to coordinate advance reservations of multiple resources. This work presents a system architecture and mechanisms to coordinate multiple advance reservations -- called co-reservations -- for delivering QoS guarantees to complex applications. We formally define the co-reservation problem as an optimization problem. The presented model supports three dimensions of freedom: the start time, the duration and the service level of a reservation. Requests and resources are described in a simple language. After matching the static properties and requirements of either side in a mapping, the reservation mechanism probes information about the future status of the resources. The versatile design of the probing step allows the efficient processing of requests, but also lets the resources express their preferences among the myriads of reservation candidates. Next, the best mapping is found through an implementation of the formal co-reservation model. Then, the mapping has to be secured, i.e., resources need to be allocated to a co-reservation candidate with all-or-nothing semantics. We study several goal-driven sequential and concurrent allocation mechanisms and define schemes for handling allocation failures. Finally, we introduce the concept of virtual resources for seamlessly embedding co-reservations into Grid resource management.}, language = {en} } @inproceedings{SchneiderGehrLinnertetal.2008, author = {Schneider, J{\"o}rg and Gehr, Julius and Linnert, Barry and R{\"o}blitz, Thomas}, title = {An Efficient Protocol for Reserving Multiple Grid Resources in Advance}, series = {Proceedings of the 3\$^rd\$ CoreGRID Workshop on Grid Middleware}, booktitle = {Proceedings of the 3\$^rd\$ CoreGRID Workshop on Grid Middleware}, address = {Barcelona, Spain}, year = {2008}, language = {en} } @inproceedings{Roeblitz2008, author = {R{\"o}blitz, Thomas}, title = {Specifying and Processing Co-Reservations in the Grid}, series = {Proceedings of the 9\$^th\$ Workshop on Parallel Systems and Algorithms}, booktitle = {Proceedings of the 9\$^th\$ Workshop on Parallel Systems and Algorithms}, address = {Dresden, Germany}, year = {2008}, language = {en} } @inproceedings{Roeblitz2008, author = {R{\"o}blitz, Thomas}, title = {Global Optimization for Scheduling Multiple Co-Reservations in the Grid}, series = {Proceedings of the CoreGRID Symposium 2008}, booktitle = {Proceedings of the CoreGRID Symposium 2008}, address = {Las Palmas de Gran Canaria, Spain}, year = {2008}, language = {en} } @article{RoeblitzSchintkeReinefeldetal.2004, author = {R{\"o}blitz, Thomas and Schintke, Florian and Reinefeld, Alexander and B{\"a}rring, Olof and Lopez, Maite Barroso and Cancio, German and Chapeland, Sylvain and Chouikh, Karim and Cons, Lionel and Poznanski, Piotr and Defert, Philippe and Iven, Jan and Kleinwort, Thorsten and Panzer-Steindel, Bernd and Polok, Jaroslaw and Rafflin, Catherine and Silverman, Alan and Smith, Tim and van Eldik, Jan and Front, David and Biasotto, Massimo and Aiftimiei, Cristina and Ferro, Enrico and Maron, Gaetano and Chierici, Andrea and dell'Agnello, Luca and Serra, Marco and Michelotto, Michele and Hess, Lord and Lindenstruth, Volker and Pister, Frank and Steinbeck, Timm and Groep, David and Steenbakkers, Martijn and Koeroo, Oscar and de Cerff, Wim and Venekamp, Gerben and Anderson, Paul and Colles, Tim and Holt, Alexander and Scobie, Alastair and George, Michael and Washbrook, Andrew and Leiva, Rafael}, title = {Autonomic Management of Large Clusters and Their Integration into the Grid}, series = {J. Grid Comput.}, volume = {2}, journal = {J. Grid Comput.}, number = {3}, doi = {10.1007/s10723-004-7647-3}, pages = {247 -- 260}, year = {2004}, language = {en} } @inproceedings{RoeblitzSchintkeWendler2004, author = {R{\"o}blitz, Thomas and Schintke, Florian and Wendler, Jan}, title = {Elastic Grid Reservations with User-Defined Optimization Policies}, series = {Proceedings of the 2nd Workshop on Adaptive Grid Middleware (AGridM'04), in conjunction with PACT 2004, Antibes Juan-les-Pins, France}, booktitle = {Proceedings of the 2nd Workshop on Adaptive Grid Middleware (AGridM'04), in conjunction with PACT 2004, Antibes Juan-les-Pins, France}, year = {2004}, language = {en} } @inproceedings{RoeblitzReinefeld2005, author = {R{\"o}blitz, Thomas and Reinefeld, Alexander}, title = {Co-reservation with the concept of virtual resources}, series = {5th International Symposium on Cluster Computing and the Grid (CCGrid 2005), 9-12 May, 2005, Cardiff, UK}, booktitle = {5th International Symposium on Cluster Computing and the Grid (CCGrid 2005), 9-12 May, 2005, Cardiff, UK}, publisher = {IEEE Computer Society}, pages = {398 -- 406}, year = {2005}, language = {en} } @inproceedings{HoegqvistRoeblitzReinefeld2007, author = {H{\"o}gqvist, Mikael and R{\"o}blitz, Thomas and Reinefeld, Alexander}, title = {Stellaris: An RDF-based Information Service for AstroGrid-D}, series = {German e-Science Conference}, booktitle = {German e-Science Conference}, publisher = {Max Planck Digital Library}, year = {2007}, language = {en} } @inproceedings{RoeblitzSchintkeReinefeld2003, author = {R{\"o}blitz, Thomas and Schintke, Florian and Reinefeld, Alexander}, title = {From Clusters to the Fabric: The Job Management Perspective}, series = {2003 IEEE International Conference on Cluster Computing (CLUSTER 2003), 1-4 December 2003, Kowloon, Hong Kong, China}, booktitle = {2003 IEEE International Conference on Cluster Computing (CLUSTER 2003), 1-4 December 2003, Kowloon, Hong Kong, China}, publisher = {IEEE Computer Society}, doi = {10.1109/CLUSTR.2003.1253351}, pages = {468 -- 473}, year = {2003}, language = {en} } @inproceedings{RoeblitzRzadca2006, author = {R{\"o}blitz, Thomas and Rzadca, Krzysztof}, title = {On the Placement of Reservations into Job Schedules}, 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 = {198 -- 210}, year = {2006}, language = {en} } @article{RoeblitzSchintkeReinefeld2006, author = {R{\"o}blitz, Thomas and Schintke, Florian and Reinefeld, Alexander}, title = {Resource reservations with fuzzy requests}, series = {Concurrency and Computation: Practice and Experience}, volume = {18}, journal = {Concurrency and Computation: Practice and Experience}, number = {13}, doi = {10.1002/cpe.1023}, pages = {1681 -- 1703}, year = {2006}, language = {en} } @inproceedings{BaerringLopezCancioetal., author = {B{\"a}rring, Olof and Lopez, Maite Barroso and Cancio, German and R{\"o}blitz, Thomas and Schintke, Florian and et al.,}, title = {Towards automation of computing fabrics using tools from the fabric management workpackage of the EU DataGrid project}, series = {Computing in High Energy and Nuclear Physics (CHEP03)}, booktitle = {Computing in High Energy and Nuclear Physics (CHEP03)}, pages = {1 -- 8}, language = {en} } @misc{EhrigDierkesSchaeferetal., author = {Ehrig, Rainald and Dierkes, Thomas and Sch{\"a}fer, Stefan and R{\"o}blitz, Susanna and Tronci, Enrico and Mancini, Toni and Salvo, Ivano and Alimguzhin, Vadim and Mari, Federico and Melatti, Igor and Massini, Annalisa and Kr{\"u}ger, Tillmann H. C. and Egli, Marcel and Ille, Fabian and Leeners, Brigitte}, title = {An Integrative Approach for Model Driven Computation of Treatments in Reproductive Medicine}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-57103}, abstract = {We present an overview of the current status of the European collaborative project PAEON. The challenge of PAEON is to provide specialists in reproduc- tive medicine with a computerised model of the menstrual cycle under normal and various pathological conditions, which will allow them to get further in- sight in fertility dynamics. This model also enables the simulation of treatment protocols, which were used within in vitro fertilization. By the definition of virtual patients through biologically admissible parametrizations our approach allows not only the evaluation of a given treatment strategy in silico, but also the design and optimization of such protocols. Once a protocol is formalized in the virtual hospital, the success can be controlled by a treatment execution monitor, which works then as a clinical decision support system. All these tools will be combined in a virtual hospital environment, enabling the access to the PAEON services through the web.}, language = {en} } @inproceedings{EhrigDierkesSchaeferetal., author = {Ehrig, Rainald and Dierkes, Thomas and Sch{\"a}fer, Stefan and R{\"o}blitz, Susanna and Tronci, Enrico and Mancini, Toni and Salvo, Ivano and Alimguzhin, Vadim and Mari, Federico and Melatti, Igor and Massini, Annalisa and Kr{\"u}ger, Tillmann H. C. and Egli, Marcel and Ille, Fabian and Leeners, Brigitte}, title = {An integrative approach for model driven computation of treatments in reproductive medicine}, series = {BIOMAT - Proceedings of the 15th International Symposium on Mathematical and Computational Biology, Rorkee, India}, booktitle = {BIOMAT - Proceedings of the 15th International Symposium on Mathematical and Computational Biology, Rorkee, India}, language = {en} } @misc{DierkesWadeNowaketal.2011, author = {Dierkes, Thomas and Wade, Moritz and Nowak, Ulrich and R{\"o}blitz, Susanna}, title = {BioPARKIN - Biology-related Parameter Identification in Large Kinetic Networks}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-12706}, number = {11-15}, year = {2011}, abstract = {Modelling, parameter identification, and simulation play an important r{\^o}le in Systems Biology. In recent years, various software packages have been established for scientific use in both licencing types, open source as well as commercial. Many of these codes are based on inefficient and mathematically outdated algorithms. By introducing the package BioPARKIN recently developed at ZIB, we want to improve this situation significantly. The development of the software BioPARKIN involves long standing mathematical ideas that, however, have not yet entered the field of Systems Biology, as well as new ideas and tools that are particularly important for the analysis of the dynamics of biological networks. BioPARKIN originates from the package PARKIN, written by P.Deuflhard and U.Nowak, that has been applied successfully for parameter identification in physical chemistry for many years.}, language = {en} } @inproceedings{ManciniSalvoMarietal., author = {Mancini, Toni and Salvo, Ivano and Mari, Federico and Melatti, Igor and Massini, Annalisa and Sinisi, Stefano and Tronci, Enrico and Davi, Francesco and Dierkes, Thomas and Ehrig, Rainald and R{\"o}blitz, Susanna and Leeners, Brigitte and Kr{\"u}ger, Tillmann H. C. and Egli, Marcel and Ille, Fabian}, title = {Patient-Specific Models from Inter-Patient Biological Models and Clinical Records}, series = {Proceedings of the 14th Conference on Formal Methods in Computer-Aided Design (FMCAD 2014)}, booktitle = {Proceedings of the 14th Conference on Formal Methods in Computer-Aided Design (FMCAD 2014)}, pages = {207 -- 214}, language = {en} } @article{DierkesRoeblitzWadeetal.2013, author = {Dierkes, Thomas and R{\"o}blitz, Susanna and Wade, Moritz and Deuflhard, Peter}, title = {Parameter identification in large kinetic networks with BioPARKIN}, series = {CoRR - Computing Research Repository - arXiv.org}, volume = {abs/1303.4928}, journal = {CoRR - Computing Research Repository - arXiv.org}, year = {2013}, language = {en} }