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2008

• Business cases. Stuttgart : Fraunhofer IRB-Verlag, 2008 (Fraunhofer Enterprise Grids) Schlagwörter: Softwaretechnik; Grid-Computing; Enterprise Grid; Vernetzung Institutsveröffentlichung: SCAI Volltext Externer Link

• Allodi, M.A.; Kirschner, Karl N.; Shields, George C.: Thermodynamics of the hydroxyl radical with isoprene. In: The journal of physical chemistry / A, Molecules, spectroscopy, kinetics, environment & general theory 112 (2008), 30, S. 7064-7071 Institutsveröffentlichung: SCAI http://dx.doi.org/10.1021/jp801869c

• Bayrasy, Pacal; Kelsall, David: Coupling of 1D and 3D simulation. In: Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 9th MpCCI User Forum : February 19th and 20th, 2008, Schloss Birlinghoven, Sankt Augustin, Germany ; proceedings. Sankt Augustin : Fraunhofer SCAI, 2008, S. 106 - 117 Institutsveröffentlichung: SCAI

• Bougé, Luc (Hrsg.); Forsell, Martti (Hrsg.); Larsson Träff, Jesper (Hrsg.); Streit, Achim (Hrsg.); Ziegler, Wolfgang (Hrsg.); Alexander, Michael (Hrsg.); Childs, Stephen (Hrsg.): Euro-Par 2007 Workshops: Parallel Processing : HPPC 2007, UNICORE Summit 2007, and VHPC 2007, Rennes, France, August 28-31, 2007 ; revised selected papers. Berlin [u.a.] : Springer, 2008 (Lecture notes in computer science; 4854) Institutsveröffentlichung: SCAI: Abteilung: BIO http://dx.doi.org/10.1007/978-3-540-78474-6

• Breton, Vincent; Jacq, Nicolas; Kasam, Vinod; Hofmann-Apitius, Martin: Grid-added value to address malaria. In: IEEE transactions on information technology in biomedicine 12 (2008), 2, S. 173-181 Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Through this paper, we call for a distributed, Internet-based collaboration to address one of the worst plagues of our present world, malaria. The spirit is a nonproprietary peer-production of information-embedding goods. And we propose to use the grid technology to enable such a worldwide "opensource" like collaboration. The first step toward this vision has been achieved during the summer 2005 on the enabling grids for E-scienceE (EGEE) grid infrastructure where 42 million ligands were docked for a total amount of 80 CPU years in 6 weeks in the quest for new drugs. The impact of this first deployment has significantly raised the interest of the research community so that several laboratories all around the world expressed interest to propose targets for a second large-scale deployment against malaria. http://dx.doi.org/10.1109/TITB.2007.895930

• Brodbeck, Carsten: MpCCI FS morphing capabilities. In: Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 9th MpCCI User Forum : February 19th and 20th, 2008, Schloss Birlinghoven, Sankt Augustin, Germany ; proceedings. Sankt Augustin : Fraunhofer SCAI, 2008, S. 36-43 Institutsveröffentlichung: SCAI

• Dunlop, R.; Arbona, T.; Rajasekaran, H.; Lo Iacono, L.; Fingberg, J.; Summers, P.; Benkner, S.; Engelbrecht, S.; Chiarini, A.; Friedrich, C.; Moore, B.; Bijlenga, P.; Iavindrasana, J.; Hose, R. D.; Frangi, A.: @neurIST - chronic disease management through integration of heterogeneous data and computer-interpretable guideline services. In: Solomonides, Tony (Hrsg.): Global healthgrid : e-science meets biomedical informatics ; proceedings of HealthGrid 2008. Amsterdam [u.a.] : IOS Press, 2008, S. 173-177 (Studies in health technology and informatics 138). Institutsveröffentlichung: SCAI: Abteilung: BIO

• Faroughi, Arash; Faroughi, Roozbeh; Wieder, Philipp; Ziegler, Wolfgang: Attributes and VOs: Extending the UNICORE authorisation capabilities. In: Bougé, Luc (Hrsg.) u.a.: Euro-Par 2007 Workshops: Parallel Processing : HPPC 2007, UNICORE Summit 2007, and VHPC 2007, Rennes, France, August 28-31, 2007 ; revised selected papers. Berlin [u.a.] : Springer, 2008 (Lecture notes in computer science 4854). Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Reliable authentication and authorisation are crucial for both service providers and their customers, where the former want to protect their resources from unauthorised access and fraudulent use while their customers want to be sure unauthorised access to their data is prevented.
  In Grid environments Virtual Organisations (VO) have been adopted as a means to organise and control access to resources and data based on roles that are assigned to users. Moreover, attribute based authorisation has emerged providing a decentralised approach with better scalability. Up to now UNICORE authentication and authorisation is based on X.509 certificates only. In this paper we will present two approaches to integrate both role or attribute based authorisation using VOMS and attribute based authorisation using Shibboleth into UNICORE.

• Friedrich, C.M.; Dach, Holger; Gattermayer, Tobias; Engelbrecht, G.; Benkner, S.; Hofmann-Apitius, Martin: @neuLink: a service-oriented application for biomedical knowledge discovery. In: Solomonides, Tony (Hrsg.): Global healthgrid : e-science meets biomedical informatics ; proceedings of HealthGrid 2008. Amsterdam [u.a.] : IOS Press, 2008, S. 165-172 (Studies in health technology and informatics 138). Institutsveröffentlichung: SCAI: Abteilung: BIO

• Friedrich, Christoph M.; Hofmann-Apitius, Martin; Dunlop, Robert; Chronakis, Ioannis; Sturkenboom, Miriam C.J.M.; Risselada, Roelof; Oliva, Baldo; Sanz, Ferran: Initial results on knowledge discovery and decision support for intracranial aneurysms. In: Proceedings of the first International Conference on Health Informatics. Setúbal : INSTICC Press, 2008, S. 265-272 (Proceedings of the first International Conference on Health Informatics 1). Schlagwörter: decision support; Bayesian networks; clinical guidelines; intracranial aneurysms Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Intracranial Aneurysms are bulbous expansions of the intracranial vessels, that may rupture and lead to subarachnoid haemorrhage, which can result in severe disability or death of the affected person. The prediction of the individual rupture risk of a patient based on information from images, haemodynamic simulations, clinical parameters and genetic markers is one of the aims of the European Integrated Project @neurIST. The predicted rupture risk is meant to support decision making on clinical treatment. We will present initial results on Knowledge Discovery through a combination of text-mining, data integration from public bioinformatics data sources, and database mining. Additionally, we provide first results for decision support through knowledge based clinical guidelines and Bayesian networks.

• Furlong, Laura I.; Dach, Holger; Hofmann-Apitius, Martin; Sanz, Ferran: OSIRISv1.2 : a named entity recognition system for sequence variants of genes in biomedical literature. In: BMC bioinformatics 9, Art. 84 (2008) Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Background: Single Nucleotide Polymorphisms, among other type of sequence variants, constitute key elements in genetic epidemiology and pharmacogenomics. While sequence data about genetic variation is found at databases such as dbSNP, clues about the functional and phenotypic consequences of the variations are generally found in biomedical literature. The identification of the relevant documents and the extraction of the information from them are hampered by the large size of literature databases and the lack of widely accepted standard notation for biomedical entities. Thus, automatic systems for the identification of citations of allelic variants of genes in biomedical texts are required. Results: Our group has previously reported the development of OSIRIS, a system aimed at the retrieval of literature about allelic variants of genes http://ibi.imim.es/osirisform.html. Here we describe the development of a new version of OSIRIS (OSIRISv1.2, http://ibi.imim.es/OSIRISv1.2.html) which incorporates a new entity recognition module and is built on top of a local mirror of the MEDLINE collection and HgenetInfoDB: a database that collects data on human gene sequence variations. The new entity recognition module is based on a pattern-based search algorithm for the identification of variation terms in the texts and their mapping to dbSNP identifiers. The performance of OSIRISv1.2 was evaluated on a manually annotated corpus, resulting in 99% precision, 82% recall, and an F-score of 0.89. As an example, the application of the system for collecting literature citations for the allelic variants of genes related to the diseases intracranial aneurysm and breast cancer is presented. Conclusion: OSIRISv1.2 can be used to link literature references to dbSNP database entries with high accuracy, and therefore is suitable for collecting current knowledge on gene sequence variations and supporting the functional annotation of variation databases. The application of OSIRISv1.2 in combination with controlled vocabularies like MeSH provides a way to identify associations of biomedical interest, such as those that relate SNPs with diseases. Volltext Externer Link http://dx.doi.org/10.1186/1471-2105-9-84

• Gosch, Thomas; Abels, Wilfried; Esins, Eric; Krämer-Fuhrmann, Ottmar; Lösekann, Wolfgang; Metsch, Thijs; Paasch, Lasse: SESIS - Entwicklung eines integrierten schiffbaulichen Entwurfs- und Simulationssystems. In: Deutschland / Bundesministerium für Wirtschaft und Technologie: BMWi-Statustagung Schifffahrt und Meerestechnik : Tagungsband, Rostock-Warnemünde, 11.12.2008. Bonn : BMWi, 2008, S. 80-96 Institutsveröffentlichung: SCAI: Abteilung: SIAN
  Abstract: Das Forschungsprojekt SESIS (Schiffentwurfs- und Simulationssystem) hat das Ziel eine strukturierte, modulare und flexible Softwareplattform für das frühe Entwurfsstadium komplexer Schiffe zu entwickeln. Zu diesem Zweck werden verschiedene Simulations- und Entwurfswerkzeuge durch die neu geschaffene Integrationsumgebung RCE unter einer nutzerfreundlichen grafische Oberfläche integriert. Dem schiffbaulichen Anwender bietet SESIS wesentliche Vorteile: - Effektive Zusammenarbeit aller Beteiligten am Entwurfsprozess durch sicheren Zugriff auf verteilte Daten und Anwendungen, - Einbindung verschiedenster "historisch gewachsener" Methoden in eine einheitliche moderne Oberfläche, - Modularer Aufbau mit der Möglichkeit, Methoden dezentral zu entwickeln und in die Entwurfsumgebung einzubinden - der einzelne Nutzer erhält damit Zugriff auf die Wissensbasis externer Experten, - Übersichtliche Verwaltung der eingebundenen Methoden und Daten, - Variabler Zugriff auf die benötigten Methoden, zentrale Lizenzverwaltung und bedarfsgerechte Abrechnung der Nutzung, - Zentrale Wartung und Pflege der Softwarebasis und verteilte Entwicklung und Anpassung der Methoden durch dezentrale Experten. Ziel des Forschungsprojektes SESIS ist es, diese Vorteile durch Einbindung ausgewählter schiffbaulicher Methoden zu demonstrieren und die Softwareplattform zu entwickeln. Das erarbeitete Nutzungskonzept ermöglicht eine nachträgliche Einbindung weiterer Partner. Volltext Postprint

• Grimme, Christian; Lepping, Joachim; Papaspyrou, Alexander; Wieder, Philipp; Yahyapour, Ramin; Oleksiak, Ariel; Wäldrich, Oliver; Ziegler, Wolfgang: Towards a standards-based Grid scheduling architecture. In: Gorlatch, Sergei (Hrsg.) u.a.: Grid computing : achievements and prospects ; selection of best papers presented at the CoreGRID Integration Workshop 2008 (CGIW 2008), which took place on 2 - 4 April 2008 in Hersonissos, Crete, Greece. New York, NY : Springer, 2008, S. 147 - 158 (CoreGrid series 9). Schlagwörter: Grid Scheduling Architecture; Scheduling Description Language; Open Grid Forum Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: The definition of a generic Grid scheduling architecture is the concern of both the Open Grid Forum's Grid Scheduling Architecture Research Group and a CoreGRID research group of the same name. Such an architecture should provide a blueprint for Grid system and middle- ware designers and assist them in linking their scheduling requirements to diverse existing solutions and standards. Based on work executed within OGF related to scheduling use cases and requirements, which tackles the problem from a more theoretical point of view, we approach in this paper the problem practically by evaluating the teikoku schedul- ing framework in the light of standards-compliance. The results of this evaluation and the existing Grid Scheduling Architecture proposal are set into context, existing gaps are described and potential solutions to bridge them are introduced. In doing so, we concentrate on the inter- operability of schedulers and the necessity of a Scheduling Description Language to achieve it.

• Gruber, Ralf; Ziegler, Wolfgang: IANOS : intelligent application-oriented scheduling for HPC Grids with IANOS. 2008 Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

• Hartt, Gregory M.; Shields, George C.; Kirschner, Karl N.: Atmospheric OCS with one to four water molecules. In: The journal of physical chemistry / A, Molecules, spectroscopy, kinetics, environment & general theory 112 (2008), 19, S. 4490-4495 Institutsveröffentlichung: SCAI http://dx.doi.org/10.1021/jp800229k

• Hofmann-Apitius, Martin; Fluck, Juliane; Furlong, Laura I.; Fornes, Oriol; Kolárik, Corinna; Hanser, Susanne; Boeker, Martin; Schulz, Stefan; Sanz, Ferran; Klinger, Roman; Mevissen, Theo; Gattermayer, Tobias; Oliva, Baldo; Friedrich, Christoph M.: Knowledge environments representing molecular entities for the virtual physiological human. In: Philosophical transactions of the Royal Society : Series A, Mathematical, physical and engineering sciences 366 (2008), 1878, S. 3091-3110 Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: In essence, the virtual physiological human (VPH) is a multiscale representation of human physiology spanning from the molecular level via cellular processes and multicellular organization of tissues to complex organ function. The different scales of the VPH deal with different entities, relationships and processes, and in consequence the models used to describe and simulate biological functions vary significantly. Here, we describe methods and strategies to generate knowledge environments representing molecular entities that can be used for modelling the molecular scale of the VPH. Our strategy to generate knowledge environments representing molecular entities is based on the combination of information extraction from scientific text and the integration of information from biomolecular databases. We introduce @neuLink, a first prototype of an automatically generated, disease-specific knowledge environment combining biomolecular, chemical, genetic and medical information. Finally, we provide a perspective for the future implementation and use of knowledge environments representing molecular entities for the VPH. http://dx.doi.org/10.1098/rsta.2008.0099

• Iavindrasana, J.; Lo Iacono, L.; Müller, H.; Periz, I.; Summers, P.; Wright, J.; Friedrich, C.M.; Dach, Holger; Gattermayer, Tobias; Engelbrecht, G.; Benkner, S.; Hofmann-Apitius, Martin; Dunlop, R.; Arbona, A.; Rajasekaran, H.; Fingberg, J.; Chiarini, A.; Moore, B.; Bijlenga, P.; Hose, R.D.; Frangi, A.: The @neurIST project. In: Solomonides, Tony (Hrsg.): Global healthgrid : e-science meets biomedical informatics ; proceedings of HealthGrid 2008. Amsterdam [u.a.] : IOS Press, 2008, S. 161-164 (Studies in health technology and informatics 138). Institutsveröffentlichung: SCAI: Abteilung: BIO

• Jacq, Nicolas; Salzemann, Jean; Legré, Yannick; Medernach, Emmanuel; Montagnat, Johan; Maaß, Astrid; Reichstadt, Matthieu; Schwichtenberg, Horst; Sridhar, Mahendrakar; Kasam, Vinod; Zimmermann, Marc; Hofmann, M.; Breton, Vincent: Grid-enabled virtual screening against malaria. In: Journal of grid computing 6 (2008), 1, S. 29-43 Institutsveröffentlichung: SCAI: Abteilung: BIO http://dx.doi.org/10.1007/s10723-007-9085-5

• Jambor, Ramon; Kasná, Blanka; Kirschner, Karl N.; Schürmann, Markus; Jurkschat, Klaus: [{2,6-(Me 2 NCH 2 ) 2 C 6 H 3 }Sn] 2 : an intramolecularly coordinated diorganodistannyne. In: Angewandte Chemie 47 (2008), 8, S. 1650-1653 Institutsveröffentlichung: SCAI http:dx.doi.org/10.1002/anie.200704635

• Joppich, Wolfgang; Pott, Sabine: Results obtained with a semi-lagrangian mass-integrating transport algorithm by using the GME grid. In: Lirkov, Ivan (Hrsg.) u.a.: Large-scale scientific computing : 6th International Conference, LSSC 2007, Sozopol, Bulgaria, June 5-9, 2007 ; revised papers. Berlin [u.a.] : Springer, 2008, S. 417-424 (Lecture notes in computer science 4818). Institutsveröffentlichung: SCAI: Abteilung: SIAN
  Abstract: The defect of mass by actual schemes within the GME has motivated the implementation of a conservative semi-Lagrangian scheme on an icosahedral mesh. This scheme for the GME-mesh is unique. The properties are demonstrated by applying the new algorithm to typical test cases as they can be derived from the shallow water test suite. The results using corse grids show: this scheme is attractive for a climate version of the GME.
  Even for periods longer than those as specified in the SWE test suite, a defect of mass in the range of accuracy of the machine is obtained. The relative error results show that the order os accuracy of the proposed algorithm is two.

• Kirschner, Karl N.; Yongye, Austin B.; Tschampel, Sarah M.; González-Outeiriño, Jorge; Daniels, Charlisa R.; Foley, B. Lachele; Woods, Robert J.: GLYCAM06: a generalizable biomolecular force field. Carbohydrates. In: Journal of computational chemistry 29 (2008), 4, S. 622-655 Institutsveröffentlichung: SCAI

• Klinger, Roman; Kolárik, Corinna; Fluck, Juliane; Hofmann-Apitius, Martin; Friedrich, Christoph M.: Detection of IUPAC and IUPAC-like Chemical Names. In: Bioinformatics 24 (2008), 13, i268-i276 Institutsveröffentlichung: SCAI: Abteilung: Bioinformatik
  Abstract: Motivation: Chemical compounds like small signal molecules or other biological active chemical substances are an important entity class in life science publications and patents. Several representations and nomenclatures for chemicals like SMILES, InChI, IUPAC or trivial names exist. Only SMILES and InChI names allow a direct structure search, but in biomedical texts trivial names and Iupac like names are used more frequent.
  While trivial names can be found with a dictionary-based approach and in such a way mapped to their corresponding structures, it is not possible to enumerate all IUPAC names. In this work, we present a new machine learning approach based on conditional random fields (CRF) to find mentions of IUPAC and IUPAC-like names in scientific text as well as its evaluation and the conversion rate with available name-to-structure tools.
  
  Results: We present an IUPAC name recognizer with an F1 measure of 85.6% on a MEDLINE corpus. The evaluation of different CRF orders and offset conjunction orders demonstrates the importance of these parameters. An evaluation of hand-selected patent sections containing large enumerations and terms with mixed nomenclature shows a good performance on these cases
  (F1 measure 81.5%). Remaining recognition problems are to detect correct borders of the typically long terms, especially when occurring in parentheses or enumerations. We demonstrate the scalability of our implementation by providing results from a full MEDLINE run.
  http://dx.doi.org/10.1093/bioinformatics/btn181

• Kolárik, Corinna; Klinger, Roman; Friedrich, Christoph M.; Hofmann-Apitius, Martin; Fluck, Juliane: Chemical names: terminological resources and corpora annotation. In: European Language Resources Association Paris: LREC 2008 : proceedings of the sixth International Language Resources and Evaluation, May 26-June 1, 2008, Marrakech, Marokko. 2008, S. 51-58 Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext Externer Link

• Krapp, Michael (Red.); Strobel, Ralf (Red.): Jahresbericht 2007 / Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI. Sankt Augustin : Fraunhofer SCAI, 2008 (Jahresbericht / Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI) Institutsveröffentlichung: SCAI Volltext

• Larson, Gregory; Deryl, Snyder; Vanden Abeele, David; Clees, Tanja: Application of single-level, pointwise algebraic, and smoothed aggregation multigrid methods to direct numerical simulations of incompressible turbulent flows. In: Computing and visualization in science 11 (2008), 1, S. 27-40 Schlagwörter: Subject Computer Science; Earth and Environmental Science and Engineering Institutsveröffentlichung: SCAI: Abteilung: NUSO.SAMG
  Abstract: Single- and multi-level iterative methods for sparse linear systems are applied to unsteady flow simulations via implementation into a direct numerical simulation solver for incompressible turbulent flows on unstructured meshes. The performance of these solution methods, implemented in the well-established SAMG and ML packages, are quantified in terms of computational speed and memory consumption, with a direct sparse LU solver (SuperLU) used as a reference. The classical test case of unsteady flow over a circular cylinder at low Reynolds numbers is considered, employing a series of increasingly fine anisotropic meshes. As expected, the memory consumption increases dramatically with the considered problem size for the direct solver. Surprisingly, however, the computation times remain reasonable. The speed and memory usage of pointwise algebraic and smoothed aggregation multigrid solvers are found to exhibit near-linear scaling. As an alternative to multi-level solvers, a single-level ILUT-preconditioned GMRES solver with low drop tolerance is also considered. This solver is found to perform sufficiently well only on small meshes. Even then, it is outperformed by pointwise algebraic multigrid on all counts. Finally, the effectiveness of pointwise algebraic multigrid is illustrated by considering a large three-dimensional direct numerical simulation case using a novel parallelization approach on a large distributed memory computing cluster. http://dx.doi.org/10.1007/s00791-006-0055-4

• Li, Jiadao; Wäldrich, Oliver; Ziegler, Wolfgang: Towards SLA-based software licenses. In: Priol, Thierry (Hrsg.) u.a.: From Grids to service and pervasive computing : 2008 CoreGRID Symposium, held August 25 - 26 in the Canary Islands, Spain. New York, NY : Springer, 2008, S. 139-152 (CoreGrid series 10). Schlagwörter: Grid; license mechanisms; service level agreements Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Software protection and licensing are important topics for both the in- dependent software vendors and software users. In Grid environments, the use of license protected applications is almost impossible and be- comes a challenging task. The reasons are twofold: (i) there are no business models of the independent software vendors for the Grid and (ii) there is no licensing technology suitable for Grid environments. In this paper, the state of the art of license management in software in- dustry as well as the current practice for managing the licenses in Grid computing is presented. The challenges and requirements of managing the software license in Grid environments are identi?ed. Two general models developed in the European pro jects BEinGRID and SmartLM for managing the software licenses in Grid computing based on service level agreement (SLA) are presented.

• Lob, Marc; Peetz, Jörg-Volker: Gekoppelte Simulationen in verteilten Rechnerumgebungen. In: Weisbecker, Anette (Hrsg.) u.a.; Fraunhofer-Gesellschaft zur Förderung der angewandten Forschung u.a.: Software. Stuttgart : Fraunhofer IRB-Verlag, 2008, S. 40-42 (Fraunhofer Enterprise Grids). Institutsveröffentlichung: SCAI

• Mei, Liquan; Thole, Clemens-August: Data analysis for parallel car-crash simulation results and model optimization. In: Simulation modelling practice and theory 16 (2008), 3, S. 329-337 Institutsveröffentlichung: SCAI http://dx.doi.org/10.1016/j.simpat.2007.11.018

• Morgan, Alexander A.; Lu, Zhiyong; Wang, Xinglong; Cohen, Aaron M.; Fluck, Juliane; Ruch, Patrick; Divoli, Anna; Fundel, Katrin; Leaman, Robert; Hakenberg, Jörg; Sun, Chengjie; Liu, Heng-hui; Rorres, Rafael; Krauthammer, Michael; Lau, William W.; Liu, Hongfang; Hsu, Chun-Nan; Schuemie, Martijn; Cohen, K. Bretonnel; Hirschman, Lynette: Overview of BioCreative II gene normalization. In: Genome biology 9 (2008), Supplement 2, S3 Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: BACKGROUND: The goal of the gene normalization task is to link genes or gene products mentioned in the literature to biological databases. This is a key step in an accurate search of the biological literature. It is a challenging task, even for the human expert; genes are often described rather than referred to by gene symbol and, confusingly, one gene name may refer to different genes (often from different organisms). For BioCreative II, the task was to list the Entrez Gene identifiers for human genes or gene products mentioned in PubMed/MEDLINE abstracts. We selected abstracts associated with articles previously curated for human genes. We provided 281 expert-annotated abstracts containing 684 gene identifiers for training, and a blind test set of 262 documents containing 785 identifiers, with a gold standard created by expert annotators. Inter-annotator agreement was measured at over 90%. RESULTS: Twenty groups submitted one to three runs each, for a total of 54 runs. Three systems achieved F-measures (balanced precision and recall) between 0.80 and 0.81. Combining the system outputs using simple voting schemes and classifiers obtained improved results; the best composite system achieved an F-measure of 0.92 with 10-fold cross-validation. A 'maximum recall' system based on the pooled responses of all participants gave a recall of 0.97 (with precision 0.23), identifying 763 out of 785 identifiers. CONCLUSION: Major advances for the BioCreative II gene normalization task include broader participation (20 versus 8 teams) and a pooled system performance comparable to human experts, at over 90% agreement. These results show promise as tools to link the literature with biological databases. http://dx.doi.org/10.1186/gb-2008-9-s2-s3 Volltext

• Müller, Thomas J.; Roy, Sudip; Wei, Zhao; Maaß, Astrid; Reith, Dirk: Economic simplex optimisation for broad range property prediction: strengths and weaknesses of an automated approach for tailoring of parameters. In: Fluid phase equilibria 274 (2008), S. 27-35 Schlagwörter: Physical property prediction; Molecular dynamics; Simplex optimization; YASP; Monte Carlo Institutsveröffentlichung: SCAI: Abteilung: SIAN
  Abstract: The need for predicting physical compound properties supplementing experimental data is considerable. Nowadays a wide range of classical simulation techniques is available for computing a multitude of such properties with acceptable effort. We here give a field report about our approach, which was to fit an initial model to a single point in the phase diagram. Byway of accessing commonly available experimental valueswe developed a compound-specific force field via simplex optimization. For predicting the desired properties of the novel model we did engage classical equilibrium as well as reverse non-equilibrium molecular dynamics in combination with Monte Carlo methods and report here the performance of these methods in detail for the example compound ethylene oxide. We find that the new model describes the experimentally observed behavior of the test compound ethylene oxide (EO) very well in the molecular dynamics section. However, when applying the simplex optimized model to the Monte Carlo section, the limits of transferability become apparent. Volltext Preprint http://dx.doi.org/10.1016/j.fluid.2008.06.009

• Peetz, Jörg-Volker; Steckel, Barbara; Ettrich Norman: Maths in flood protection. In: ERCIM News (2008), 73, S. 23-24 Schlagwörter: 3ZM-GRIMEX; MpCCI; flood simulation; code coupling Institutsveröffentlichung: SCAI
  Abstract: The 2002 flooding of the Elbe River in Dresden, Germany, showed that apart from the obvious destruction caused by surface water, considerable damage was caused by groundwater and water from the sewer system. Groundwater levels can rise quickly due to overflowing sewers or above-ground flow, causing basement flooding and structural damage to houses. Thus, a coupled simulation of the three components surface water, groundwater and the sewer system is important for flood risk management. Volltext externer Link

• Pichot, Antoine; Wieder, Philipp; Wäldrich, Oliver; Ziegler, Wolfgang: Dynamic SLA Negotiation based on WS-Agreement. In: Cordeiro, José (Hrsg.) u.a.; Institute for Systems and Technologies of Information, Control and Communication Setúbal: WEBIST 2008 : proceedings of the 4th International Conference on Web Information Systems and Technologies. Setúbal : Insticc Press, 2008 Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: In Grid, e-Science and e-Business environments Service Level Agreements (SLAs) are often used to establish frameworks for the delivery of services between service providers and the home organisations of the customers.
  While this high level SLAs, e.g. framework contracts, govern the relationship between the parties, it is desirable for the end-user to have dedicated quality of service (QoS) also for individual services like the orchestration of resources necessary for composed services. Grid level scheduling services typically are responsible for the orchestration and coordination of resources in the Grid, which requires the Grid level scheduler to coordinate resource management systems probably located in different domains. As the site autonomy has to be respected negotiating with the individual sites is the only way to achieve the intended coordination.
  Electronic SLAs emerged as a new way to negotiate and manage usage of resources in the Grid and are already adopted by a number of management systems. Therefore, it is natural to look for ways to adopt SLAs for Grid level scheduling. To realise this approach we need efficient and flexible protocols supporting dynamic negotiation and creation of SLAs. In this paper we propose and discuss ongoing work on extensions to the WS-Agreement protocol addressing these issues. Volltext

• Prätzel-Wolters, Dieter; Trottenberg, Ulrich: Mathematik - Schlüssel zu Innovationen. In: Fraunhofer-Magazin / dt. Ausgabe (2008), 4, Beilage: Mathematik erleben, S. 2-3 Institutsveröffentlichung: SCAI

• Qu, C.; Zimmermann, Falk; Kumpf, Kai; Kamuzinzi, R.; Ledent, V.; Herzog, R.: Semantics-enabled service discovery framework in the SIMDAT pharma grid. In: IEEE transactions on information technology in biomedicine 12 (2008), 2, S. 182-190 Institutsveröffentlichung: SCAI
  Abstract: We present the design and implementation of a semantics-enabled service discovery framework in the data Grids for process and product development using numerical simulation and knowledge discovery (SIMDAT) Pharma Grid, an industry-oriented Grid environment for integrating thousands of Grid-enabled biological data services and analysis services. The framework consists of three major components: the Web ontology language (OWL)-description logic (DL)-based biological domain ontology, OWL Web service ontology (OWL-S)-based service annotation, and semantic matchmaker based on the ontology reasoning. Built upon the framework, workflow technologies are extensively exploited in the SIMDAT to assist biologists in (semi)automatically performing in silico experiments. We present a typical usage scenario through the case study of a biological workflow: IXodus. http://dx.doi.org/10.1109/TITB.2007.907987

• Rajasekaran, H.; Lo Iacono, L.; Hasselmeyer, P.; Fingberg, J.; Summers, P.; Benkner, S.; Engelbrecht, G.; Arbona, A.; Chiarini, A.; Friedrich, C.M.; Hofmann-Apitius, Martin; Kumpf, K.; Moore, B.; Bijlenga, P.; Iavindrasana, J.; Mueller, H.; Hose, R.D.; Dunlop, R.; Frangi, A.: @neurIST - Towards a system architecture for advanced disease management through integration of heterogeneous data, computing, and complex processing services. In: Computer Society / Technical Committee on Computational Medicine: 21st IEEE International Symposium on Computer-Based Medical Systems : CBMS '08 ; 17 - 19 June 2008, Jyväskylä, Finland ; proceedings. Los Alamitos, Calif. [u.a.] : IEEE Computer Society Press, 2008, S. 361-366 Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: This paper presents the system architecture of the @neurIST project, which aims at supporting the research and treatment of cerebral aneurysms by bringing together heterogeneous data, computing and complex processing services. The architecture is generic enough to adapt it to the treatment of other diseases beyond cerebral aneurysms. The paper describes the generic requirements of the system and presents the architecture, applications and middleware technologies used to realise the system and highlights the innovations in @neurIST. http://dx.doi.org/10.1109/CBMS.2008.42

• Rasheed, Hassan; Gruber, Ralf; Keller, Vincent; Kuonen, Pierre; Wieder, Philipp; Wäldrich, Oliver; Ziegler, Wolfgang: IANOS: an intelligent application oriented scheduling framework for an HPCN Grid. In: Gorlatch, Sergei (Hrsg.) u.a.: Grid computing : achievements and prospects ; selection of best papers presented at the CoreGRID Integration Workshop 2008 (CGIW 2008), which took place on 2 - 4 April 2008 in Hersonissos, Crete, Greece. New York, NY : Springer, 2008, S. 237-248 (CoreGrid series 9). Schlagwörter: High Performance Computing; Grid Scheduling; Meta Scheduling Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: We present the architecture and implementation of IANOS middleware that is a result of integration of the Intelligent Scheduling Service into the VIOLA meta-scheduling environment. The goal of the new, integrated environment is to provide a general middleware infrastructure allowing optimal positioning and scheduling of HPC Grid applications. The scheduling algorithms used to calculate best-suited resources are based on an objective cost function that exploits information on the parameterization of applications and resources. The overall middleware architecture comprises four general services and two modules. The implementation is based on state-of-the-art Grid and Web services technology as well as existing and emerging standards (WSRF, WS-Agreement, JSDL, and GLUE). IANOS in general is agnostic to a Grid middleware. Currently, the IANOS integration with the Unicore Grid system is under development.

• Ruau, David; Kolárik, Corinna; Mevissen, Heinz-Theodor; Müller, Emmanuel; Assent, Ira; Krieger, Ralph; Seidl, Thomas; Hofmann-Apitius, Martin; Zenke, Martin: Public microarray repository semantic annotation with ontologies employing text mining and expression profile correlation. In: BMC bioinformatics 9 (2008), Supplement 10, Art. 05 Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext Externer link http://dx.doi.org/10.1186/1471-2105-9-S10-O5

• Scholz, Joachim; Toska, Karen; Luborzewski, Alexander; Maaß, Astrid; Schünemann, Volker; Haavik, Jan; Moser, Andreas: Endogenous tetrahydroisoquinolines associated with Parkinson's disease mimic the feedback inhibition of tyrosine hydroxylase by catecholamines. In: The FEBS journal 275 (2008), 9, S. 2109-2121 Institutsveröffentlichung: SCAI: Abteilung: SIAN
  Abstract: N-methyl-norsalsolinol and related tetrahydroisoquinolines accumulate in the nigrostriatal system of the human brain and are increased in the cerebrospinal fluid of patients with Parkinson's disease. We show here that 6,7-dihydroxylated tetrahydroisoquinolines such as N-methyl-norsalsolinol inhibit tyrosine hydroxylase, the key enzyme in dopamine synthesis, by imitating the mechanisms of catecholamine feedback regulation. Docked into a model of the enzyme's active site, 6,7-dihydroxylated tetrahydroisoquinolines were ligated directly to the iron in the catalytic , occupying the same position as the catecholamine inhibitor dopamine. In this position, the ligands competed with the essential tetrahydropterin cofactor for access to the active site. Electron paramagnetic resonance spectroscopy revealed that, like dopamine, 6,7-dihydroxylated tetrahydroisoquinolines rapidly convert the catalytic iron to a ferric (inactive) state. Catecholamine binding increases the thermal stability of tyrosine hydroxylase and improves its resistance to proteolysis. We observed a similar effect after incubation with N-methyl-norsalsolinol or norsalsolinol. Following an initial rapid decline in tyrosine hydroxylation, the residual activity remained stable for 5 h at 37 °C. Phosphorylation by protein kinase A facilitates the release of bound catecholamines and is the most prominent mechanism of tyrosine hydroxylase reactivation. Protein kinase A also fully restored enzyme activity after incubation with N-methyl-norsalsolinol, demonstrating that tyrosine hydroxylase inhibition by 6,7-dihydroxylated tetrahydroisoquinolines mimics all essential aspects of catecholamine end-product regulation. Increased levels of N-methyl-norsalsolinol and related tetrahydroisoquinolines are therefore likely to accelerate dopamine depletion in Parkinson's disease. http://dx.doi.org/10.1111/j.1742-4658.2008.06365.x

• Schwarz, Fritz: ALLTYPES in the Web. In: ACM communications in computer algebra 42 (2008), 165/166, S. 185-187 Institutsveröffentlichung: SCAI: Abteilung: INA

• Schwarz, Fritz: Loewy Decomposition of Third-Order Linear PDE's. In: Gonzales-Vega, L. (Hrsg.); Association for Computing Machinery / Special Interest Goup on Symbolic and Algebraic Manipulation: ISSAC 2008 : proceedings of the 2008 ACM-SIGSAM International Symposium on Symbolic and Algebraic Computation, July 20-23, 2008, Hagenberg, Austria. New York, NY : ACM, 2008, S. 277-286 Schlagwörter: Partial Differential Equations; Computer Algebra Institutsveröffentlichung: SCAI
  Abstract: Loewy's decomposition of a linear ordinary differential operator as the product of largest completely reducible components is generalized to partial differential operators of order three in two variables. This is made possible by considering the problem in the ring of partial differential operators where both left intersections and right divisors of left ideals are not necessarily principal. Listings of possible decomposition types are given. Many of them are illustraded by worked out examples. Algorithmic questions and questions of uniqueness are discussed in the Summary.

• Seidel, Jan; Wäldrich, Oliver; Wieder, Philipp; Yahyapour, Ramin; Ziegler, Wolfgang: Using SLA for Resource Management and Scheduling - A Survey. In: Talia, Domenico (Hrsg.) u.a.: Grid Middleware and Services : Challenges and Solutions. New York, NY [u.a.] : Springer, 2008 (CoreGrid series 8). Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Service Level Agreements may be used to establish agreements on the quality of a service between a service provider and a service consumer. The roles of service provider and service consumer may realised in different shapes ranging from individuals to institutions, software agents or other systems acting on behalf of physical entities or steered by those. This paper gives an overview on the state of the art using Service Level Agreements in the domain of Scheduling and Resource Management. An introduction is given where Service Level Agreements are considered, the technologies used, and what should be accomplished followed by descriptions of the systems that already explicitly implement and use Service Level Agreements.
  

• Shahid, Mohammad; Ziegler, Wolfgang; Kasam, Vinod; Zimmermann, Marc; Hofmann-Apitius, Martin: Virtual High Throughput Screening (vHTS) on an optical high speed testbed. In: Solomonides, Tony (Hrsg.): Global healthgrid : e-science meets biomedical informatics ; proceedings of HealthGrid 2008. Amsterdam [u.a.] : IOS Press, 2008, S. 125-134 (Studies in health technology and informatics 138). Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Malaria remains a global health concern, which kills over a million people each year. In this paper we present work extending the approach of the WISDOM initiative by focusing on the problems noticed during the first WISDOM challenge against malaria and test the newly established, high bandwidth optical Grid environment VIOLA for advanced bioinformatics applications using the UNICORE middleware service. In addition we present an approach to reduce the size of the compound database to improve the efficiency of the screening.

• Sherer, E.C.; Kirschner, Karl N.; Pickard, F.C.; Rein, C.; Feldgus, S.; Shields, G.C.: Efficient and accurate characterization of the Bergman cyclization for several enediynes including an expanded substructure of esperamicin A(1). In: The journal of physical chemistry / B, Condensed matter, materials, surfaces, interfaces & biophysical chemistry 112 (2008), 51, S. 16917-16934 Institutsveröffentlichung: SCAI http://dx.doi.org/10.1021/jp807341t

• Smith, Larry; Tanabe, Lorraine K.; Johnson nee Ando, Rie; Juo, Cheng-Ju; Chung, I-Fang; Hsu, Chun-Nan; Lin, Yu-Shi; Klinger, Roman; Friedrich, Christoph M.; Ganchev, Kuzman; Torii, Manabu; Liu, Hongfang; Haddow, Barry; Struble, Craig A.; Povinelli, Richard J.; Vlachos, Andreas; Baumgartner Jr., William A.; Hunter, Lawrence; Carpenter, Bob; Tsai, Richard Tzong-Han; Dai, Hong jie; Liu, Feng; Chen, Yifei; Sun, Chengjie; Katrenko, Sophia; Adriaans, Pieter; Blaschke, Christian; Torres Perez, Rafel; Neves, Mariana; Nakov, Preslav; Divoli, Anna; Mana, Manuel; Mata-Vazquez, Jacinto; Wilbur, John: Overview of BioCreative II gene mention recognition. In: Genome biology 9 (2008), Supplement 2 Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop. In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions. A variety of different methods were used and the results varied with a highest achieved F1 score of 0.8721. Here we present brief descriptions of all the methods used and a statistical analysis of the results. We also demonstrate that, by combining the results from all submissions, an F score of 0.9066 is feasible, and furthermore that the best result makes use of the lowest scoring submissions. http://dx.doi.org/10.1186/gb-2008-9-s2-s2 Volltext

• Steffes-lai, Daniela; Thole, Clemens-August; Nikitin, Igor; Nikitina, Lialia: Interactive Optimization with DesParO. In: ERCIM News (2008), 73, S. 29-30 Institutsveröffentlichung: SCAI: Abteilung: NUSO
  Abstract: Product optimization is an important step in the process of product development. How does the behaviour of a product change when certain parameters are varied? The answer is given by the optimization environment DesParO. Volltext Externer Link

• Stork, André; Thole, Clemens-August; Klimenko, Stanislav; Nikitin, Igor; Nikitina, Lialia; Astakhov, Yuri: Towards interactive simulation in automotive design. In: The visual computer 24 (2008), 11, S. 947-953 Institutsveröffentlichung: SCAI

• Talia, Domenico (Hrsg.); Yahyapour, Ramin (Hrsg.); Ziegler, Wolfgang (Hrsg.): Grid Middleware and Services : Challenges and Solutions. New York, NY [u.a.] : Springer, 2008 (CoreGrid series; 8) Institutsveröffentlichung: SCAI: Abteilung: BIO

• Thole, Clemens-August: PICKEffizienter Austausch von Simulationsergebnissen mit FEMZIP. In: Weisbecker, Anette (Hrsg.) u.a.; Fraunhofer-Gesellschaft zur Förderung der angewandten Forschung u.a.: Software. Stuttgart : Fraunhofer IRB-Verlag, 2008, S. 43-45 (Fraunhofer Enterprise Grids). Institutsveröffentlichung: SCAI

• Trottenberg, Ulrich: Begeisterung durch Anwendungen und Algorithmen. In: Der mathematische und naturwissenschaftliche Unterricht 61 (2008), 4 Institutsveröffentlichung: SCAI

• Trottenberg, Ulrich: Mathematik ist Technologie : Essay. In: Fraunhofer-Magazin / dt. Ausgabe (2008), 1, S. 30-31 Institutsveröffentlichung: SCAI

• Trottenberg, Ulrich; Prätzel-Wolters, Dieter: Rechnen für Fortschritt und Zukunft - Innovationen brauchen Mathematik. In: Jahresbericht 2007 / Fraunhofer-Gesellschaft FhG. München : FhG, 2008, S. 47-55 (Jahresbericht / Fraunhofer-Gesellschaft FhG). Institutsveröffentlichung: SCAI

• Trottenberg, Ulrich: Das Superrechnerprojekt SUPRENUM (1984-1989). In: Reuse, Bernd (Hrsg.) u.a.: Informatikforschung in Deutschland. Berlin [u.a.] : Springer, 2008, Kap. 2.3, pp.176-187 Institutsveröffentlichung: SCAI

• Tyagi, Sandeep; Arnold, Axel; Holm, Christian: Electrostatic layer correction with image charges: A linear scaling method to treat slab 2D+h systems with dielectric interfaces. In: The journal of chemical physics 129 (2008), 20, Art. 204102, 9 S. Schlagwörter: bioelectric potentials; cellular biophysics; dielectric materials; electrostatics; time-varying systems Institutsveröffentlichung: SCAI: Abteilung: SIAN
  Abstract: A fast algorithm for dealing with electrostatic interactions in partially periodic systems that are confined along the nonperiodic direction by two planar dielectric interfaces is presented. The method is a generalization of the electrostatic layer correction (ELC) method of Arnold et al. [J. Chem. Phys. 117, 2496 (2002)], and employs an exact relation between the 2D+h system and a three-dimensional (3D) periodic system. The terms connecting the two systems can be evaluated linearly in the number of charges. Thus, the method shows overall the scaling of the underlying method employed to handle the Coulombic 3D case. Moreover, our algorithm can accurately handle multiple polarization image charges due to the dielectric interfaces as well as all the periodic images due to the periodic boundary conditions and has full control over the errors depending on the underlying method used for the 3D periodic case. http://dx.doi.org/10.1063/1.3021064 Volltext Postprint

• Väänänen, Jouko; Trottenberg, Ulrich: Maths for everyday life. In: ERCIM News (2008), 73, S. 10-11 Institutsveröffentlichung: SCAI Volltext Externer Link

• Weisbecker, Anette (Hrsg.); Pfreundt, Franz-Josef (Hrsg.); Linden, Johannes (Hrsg.); Unger, Steffen (Hrsg.); Fraunhofer-Gesellschaft zur Förderung der angewandten Forschung u.a.: Grid check. Stuttgart : Fraunhofer IRB-Verlag, 2008 (Fraunhofer Enterprise Grids) Institutsveröffentlichung: SCAI Volltext Externer Link

• Weisbecker, Anette (Hrsg.); Pfreundt, Franz-Josef (Hrsg.); Linden, Johannes (Hrsg.); Unger, Steffen (Hrsg.); Fraunhofer-Gesellschaft zur Förderung der angewandten Forschung u.a.: Software. Stuttgart : Fraunhofer IRB-Verlag, 2008 (Fraunhofer Enterprise Grids) Institutsveröffentlichung: SCAI Volltext Externer Link

• Wieder, Philipp; Ziegler, Wolfgang; Keller, Vincent: IANOS - efficient use of HPC Grid resources. In: ERCIM News (2008), 74 : Special issue, S. 27-29 Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext externer Link

• Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 9th MpCCI User Forum : February 19th and 20th, 2008, Schloss Birlinghoven, Sankt Augustin, Germany ; proceedings. Sankt Augustin : Fraunhofer SCAI, 2008 Institutsveröffentlichung: SCAI

• Ziegler, Wolfgang: Phosphorus : a European optical Grid test-bed. 2008 Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

2007

• Algorri, Maria-Elena; Zimmermann, Marc; Friedrich, Christoph M.; Akle, Santiago; Hofmann-Apitius, Martin: Reconstruction of Chemical Molecules from Images. In: Engineering in Medicine and Biology Society u.a.: 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society : EMBC 2007, 22 - 26 Aug. 2007, Lyon, France ; in conjunction with the biennial conference of the Société Française de Génie Biologique et Médical (SFGBM). Piscataway, NJ : IEEE Service Center, 2007, S. 4609-4612 Institutsveröffentlichung: SCAI: Abteilung: Bioinformatik http://dx.doi.org/10.1109/IEMBS.2007.4353366

• Arbona, A.; Benkner, S.; Engelbrecht, G.; Fingberg, J.; Hoffmann, M.; Kumpf, Kai; Lonsdale, G.; Woehrer, A.: A service-oriented grid infrastructure for biomedical data and com-pute services. In: IEEE transactions on nanobioscience 6 (2007), 2, S. 136-141 Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Service-oriented Grid technologies are increasingly utilized for the realization of future biomedical IT infrastructures since they offer unprecedented opportunities for the integration of advanced analysis and simulation applications as well as distributed heterogeneous data sources and information systems. The European Union's @neurIST project is developing a Grid-based IT infrastructure for the management of all processes linked to research, diagnosis, and treatment development for complex and multifactorial diseases encompassing data repositories, computational analysis services, and information systems handling multiscale, multimodal information at distributed sites. This paper provides an overview of the @neurIST Grid middleware and outlines the infrastructure offered for the provision of advanced compute and data services to support computationally demanding modeling and simulation tasks and to access heterogeneous distributed data sources through semantic integration. http://dx.doi.org/10.1109/TNB.2007.897438

• Barz, Christoph; Eickermann, Thomas; Pilz, Markus; Wäldrich, Oliver; Westphal, Lidia; Ziegler, Wolfgang: Co-Allocating Compute and Network Resources - Bandwidth on Demand in the VIOLA Testbed. In: Priol, Thierry (Hrsg.) u.a.: Towards next generation grids : proceedings of the CoreGrid Symposium 2007, August 27-28, 2007, Rennes, France. New York, NY [u.a.] : Springer, 2007, S. 193-202 Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Distributed applications or workflows need to access and use compute, storage and network resources simultaneously or chronologically coordinated respectively. Examples are distributed multi-physics simulations that use the combined computational performance and data storage of multiple clusters.
  A coordinated reservation and allocation of the resources is a prerequisite for the efficient use of such resources.
  This contribution describes the components of a system that provides Grid users with this functionality. The Grid middleware UNICORE is extended to access a MetaScheduling Service (MSS) performing orchestration of resources of different administrative domains, using advance reservation capability of local resource management systems (RMS) - including network connections for which ARGON serves as RMS. ARGON leverages Bandwidth on Demand, a cornerstone of next generation Grid enabled optical networks rendering the network to a first class Grid resource.

• Baturin, J.M.; Goebel, M.; Klimenko, S.V.; Leonov, A.V.; Nikitin, Igor N.; Nikitina, L.D.; Serebrov, A.A.; Urazmetov, V.F.: Virtual Storytelling as Innovative Educational Technology. In: Moscow Institute for Physics and Technology / Chair of System Integration and Management: Annals of SIM. Moscow : ICPT, 2007 Institutsveröffentlichung: SCAI: Abteilung: NUSO

• Biskup, Joachim; Tsatedem, Christian; Wiese, Lena: Secure mediation of join queries by processing ciphertexts. In: 2007 IEEE 23rd International Conference on Data Engineering workshop. Piscataway, NJ : IEEE Service Center, 2007, S. 715-724 (2007 IEEE 23rd International Conference on Data Engineering workshop 2). Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: In a secure mediated information system, confidentiality is one of the main concerns when transmitting data from datasources to clients via a mediator. We present three approaches that allow a mediator to compute a JOIN operation on encrypted relations; each approach uses a different encryption scheme. We adapt these schemes to the mediator architecture and provide a comprehensive description of the resulting protocols. A first security analysis is also given. http://doi.ieeecomputersociety.org/10.1109/ICDEW.2007.4401059

• Clees, Tanja; Ganzer, Leonhard: An efficient algebraic multi-grid solver strategy for adaptive implicit methods in oil reservoir simulation. In: Society of Petroleum Engineers United States: SPE Reservoir Simulation Symposium 2007 : February 26 -28, 2007, Houston, Texas, USA. SPE, 2007 Institutsveröffentlichung: SCAI: Abteilung: NUSO.SAMG
  Abstract: We propose a new, efficient, adaptive algebraic multigrid (AMG) solver strategy for the discrete systems of partial differential equations arising from structured or unstructured grid models in reservoir simulation. The proposed strategy has been particularly tailored to linear systems of equations arising in adaptive implicit methods. The coarsening process of the AMG method designed automatically employs information on the physical structure of the models; as a smoother, an adaptive ILUT method is employed, taking care of an efficient solution of the hyperbolic parts whilst providing adequately smooth errors for the elliptic parts. To achieve a good compromise of high efficiency and robustness for a variety of problem classes - ranging from simple, small black-oil to challenging, large compositional models - an automatic, adaptive ILUT parameter and AMG solver switching strategy, alpha-SAMG, has been developed. Its efficiency is demonstrated for eight industrial benchmark cases by comparison against standard one-level and AMG solvers as well as the pure one-level variant of the proposed new strategy. In addition, very promising results of first parallel runs are shown.

• Drotz, Alain; Gruber, Ralf; Keller, Vincent; Thiémard, Michela; Tolou, Ali; Tran, Trach-Minh; Cristiano, Kevin; Kuonen, Pierre; Wieder, Philipp; Wäldrich, Oliver; Ziegler, Wolfgang; Manneback, Pierre; Schwiegelshohn, Uwe; Yahyapour, Ramin; Kunszt, Peter; Maffioletti, Sergio; Sawley, Marie-Christine; Witzig, Christoph; CoreGrid - European Research Network on Foundations, Software Infrastructures and Applications for Large Scale Distributed, GRID and Peer-to-Peer Technologies; Institute on Resource Management and Scheduling: Application-oriented scheduling for HPC Grids. CoreGrid, 2007 (CoreGrid technical report; TR-0070) Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

• Eickermann, Thomas; Frings, Wolfgang; Wäldrich, Oliver; Wieder, Philipp; Ziegler, Wolfgang; Institute on Resource Management and Scheduling; CoreGrid - European Research Network on Foundations, Software Infrastructures and Applications for Large Scale Distributed, GRID and Peer-to-Peer Technologies: Co-allocation of MPI Jobs with the VIOLA Grid MetaScheduling Framework. 2007 (CoreGrid technical report; TR-0081) Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: The co-allocation of resources for the parallel execution of distributed MPI applications in a Grid environment is a challenging task. On the hand it is mandatory to co-ordinate the usage of computational resources, like for example compute clusters, on the other hand improves the additional scheduling of network resources the overall performance. Most Grid middlewares do not include such meta-scheduling capabilities, but rely on the provision of higher-level, often domain-specific, services. In this paper we describe the integration of a meta-scheduler, namely the VIOLA MetaScheduling Service, into an existing Grid middleware to provide a framework for co-allocation of MPI jobs. For these purposes, the design and architecture of the framework are presented and, based on the MetaTrace application, the performance of the system is evaluated. Volltext

• Eickermann, Thomas; Frings, Wolfgang; Wäldrich, Oliver; Wieder, Philipp; Ziegler, Wolfgang: Co-allocation of MPI Jobs with the VIOLA Grid MetaScheduling Framework. In: German e-Science Conference 2007 : GES 2007, 2. - 4. Mai 2007, Baden-Baden. 2007, 10 S. Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: The co-allocation of resources for the parallel execution of distributed MPI applications in a Grid environment is a challenging task. On the hand it is mandatory to co-ordinate the usage of computational resources, like for example compute clusters, on the other hand improves the additional scheduling of network resources the overall performance. Most Grid middlewares do not include such meta-scheduling capabilities, but rely on the provision of higher-level, often domain-specific, services. In this paper we describe the integration of a meta-scheduler, namely the VIOLA MetaScheduling Service, into an existing Grid middleware to provide a framework for co-allocation of MPI jobs. For these purposes, the design and architecture of the framework are presented and, based on the MetaTrace application, the performance of the system is evaluated. Volltext

• Ettrich Norman; Eulitz, Katja; Müller, Mike; Peetz, Jörg-Volker; Sommer, Thomas; Steckel, Barbara: 3-Code Coupling in Flood Simulation. In: Wolf, Klaus Dieter (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 8TH MpCCI User Forum 2007 : February 13 and 14, 2007, Sankt Augustin ; proceedings. Sankt Augustin : Fraunhofer SCAI, 2007, S. 108-117 Schlagwörter: 3ZM-GRIMEX; flood simulation; coupling, MPCCI Institutsveröffentlichung: SCAI: Abteilung: SIAN
  Abstract: The flood 2002 at the Elbe River showed that besides the apparent damages by surface waters, considerable damage was caused by groundwater and waters from the sewer system. Fast rising groundwater levels due to infiltration of overland flow or water from the sewer system can damage basements and can be a serious thread to the static of houses. The objective of the project 3ZM-GRIMEX is the development of a software system for the coupled simulation of three components: surface water, groundwater, and sewer water. The coupled system will be used in flood risk management. The implementation of the software system is based on MpCCI. Exchanged quantities are water heights and water fluxes between the components. The paper describes the coupled software system and the involved application codes with emphasis on the requirements for MpCCI. Challenges include that all application codes are interacting with each other, the codes are 1-, 2- as well as 3-dimensional, and the time-scales in the codes are very different. Furthermore, the paper outlines the use of MpCCI, including the development of suitable code adaptors with a coupling driver, the time step negotiation, the coupling algorithm, and a dummy code used for tests and as substitute. Finally, numerical results for a generic test model will be given. Simulations of the flood 2002 at Dresden are planned for 2007.

• Faroughi, Arash; Faroughi, Roozbeh; Wieder, Philipp; Ziegler, Wolfgang; CoreGrid - European Research Network on Foundations, Software Infrastructures and Applications for Large Scale Distributed, GRID and Peer-to-Peer Technologies: Attributes and VOs: Extending the UNICORE authorisation capabilities. 2007 (CoreGrid technical report; TR-0097) Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Reliable authentication and authorisation are crucial for both service providers and their customers, where the former want to protect their resources from unauthorised access and fraudulent use while their customers want to be sure unauthorised access to their data is prevented.
  In Grid environments Virtual Organisations (VO) have been adopted as a means to organise and control access to resources and data based on roles that are assigned to users. Moreover, attribute based authorisation has emerged providing a decentralised approach with better scalability. Up to now UNICORE authentication and authorisation is based on X.509 certificates only. In this paper we will present two approaches to integrate both role or attribute based authorisation using VOMS and attribute based authorisation using Shibboleth into UNICORE. Volltext

• Figuerola, S.; Ciulli, N.; Leenheer, M. de; Demchenko, Y.; Ziegler, Wolfgang; Binczewski, A.: PHOSPHORUS: Single-step on-demand services. In: Wang, Jianli (Hrsg.) u.a.; Society of Photo-optical Instrumentation Engineers: Network Architectures, Management, and Applications V : SPIE Asia-Pacific Optical Communications (APOC), Wuhan, China, Nov. 1-5, 2007 ; proceedings. Bellingham, Wash. : SPIE, 2007, 16 S. (Proceedings of SPIE 6784). Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: The Phosphorus project focuses on delivering advanced network services to Grid users and applications interconnected by heterogeneous infrastructures. The project is addressing some of the key technical challenges to enable on-demand end-to-end network services across multiple domains. The Phosphorus network concept makes applications aware of their complete Grid resources environment -computational and networking- and its capabilities. Phosphorus enables and tests dynamic adaptive and optimised use of the heterogeneous network infrastructure interconnecting various high-end resources. The project will demonstrate on-demand service delivery across access-independent multi-domain/multi- vendor research network test-beds on a European and worldwide scope.
  Phosphorus enhances and demonstrates
  solutions that facilitate vertical and horizontal communication among applications middleware and the network resources across different domains, managed by existing Network Resource Provisioning Systems (NRPS), or domains that integrate a new Grid-GMPLS (G2MPLS) Control Plane, both under a new AAA architecture to support policy based on- demand network resource provisioning. This G2MPLS extends ASON/GMPLS in order to provide part of the functionalities related to the selection, co-allocation and maintenance of both Grid and network resources, by exposing upgraded interfaces at the UNI and E-NNI network reference points -i.e.
  G.OUNI and G.E-NNI-. The project outcomes are going to be demonstrated in a worldwide test-bed.
  Volltext

• Fluck, Juliane; Mevissen, T.H.; Dach, H.; Oster, M.; Hofmann-Apitius, Martin: ProMiner: recognition of human gene and protein names using regularly updated dictionaries. In: Hirschmann, Lynette (Hrsg.) u.a.: Proceedings of the Second BioCreative Challenge Evaluation Workshop : April 23-25 2007, Madrid, Spain. Madrid, 2007, S. 149-151 Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

• Frangi, Alejandro F.; Ruiz, Aurelio; Hofmann-Apitius, Martin: Understanding S. Cerebral Aneurysms - The @neurIST Project. In: ERCIM News (2007), 69, S. 16-17 Institutsveröffentlichung: SCAI Volltext Externer Link

• Gietz, Peter; Grimm, Christian; Groeper, Ralf; Haase, Martin; Makedanz, Siegfried; Pfeiffenberger, Hans; Schiffers, Michael; Ziegler, Wolfgang: Trust Issues in Shibboleth-Enabled Federated Grid Authentication and Authorization Infrastructures Supporting Multiple Grid Middlewares. In: e-Science 2007 : 3rd IEEE International Conference on e-Science and Grid Computing, Bangalore, India, December 10th - 13th 2007. New York, NY : IEEE, 2007 Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: In Germany's D-Grid project numerous Grid communities are working together to develop a common overarching Grid. One major aim of D-Grid is thus to integrate the existing Grid deployments and make them interoperable. The major challenge in this endeavor lies in the heterogeneity of the current
  implementations: Three Grid middleware and different VO management approaches have to be orchestrated to achieve the intended interoperability. This paper presents some of the findings of the IVOM project regarding VO management technologies. Furthermore, options are discussed for making Shibboleth federations and VO management systems interoperable so that attributes from both sources can be used for authentication and authorization in Grids. Finally two approaches, one using a so called \"trust proxy\" and one without trust proxying, are presented and support by current Grid middleware is discussed.

• Grimme, Christian; Lepping, Joachim; Papaspyrou, Alexander; Wieder, Philipp; Yahyapour, Ramin; Oleksiak, Ariel; Wäldrich, Oliver; Ziegler, Wolfgang; CoreGrid - European Research Network on Foundations, Software Infrastructures and Applications for Large Scale Distributed, GRID and Peer-to-Peer Technologies; Institute on Resource Management and Scheduling: Towards a standards-based Grid Scheduling Architecture. CoreGrid, 2007 (CoreGrid technical report; TR-0123) Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

• Gruber, Ralf; Keller, Vincent; Thiémard, Michela; Wäldrich, Oliver; Wieder, Philipp; Ziegler, Wolfgang; Manneback, Pierre: Integration of grid cost model into ISS/VIOLA meta-scheduler environment. In: Lehner, Wolfgang (Hrsg.) u.a.: Euro-Par 2006 workshops: parallel processing : CoreGRID 2006, UNICORE Summit 2006, petascale computational biology and bioinformatics, Dresden, Germany, August 29 - September 1, 2006. Berlin [u.a.] : Springer, 2007, S. 215-224 (Lecture notes in computer science 4375). Institutsveröffentlichung: SCAI: Abteilung: BIO http.//dx.doi.org/10.1007/978-3-540-72337-0%5F21 Volltext

• Harmandaris, Vagelis A.; Reith, Dirk; Vegt, Nico F. A. van der; Kremer, Kurt: Comparison between coarse-graining models for polymer systems : two mapping schemes for polystyrene. In: Macromolecular chemistry and physics 208 (2007), 19-20, S. 2109-2120 Institutsveröffentlichung: SCAI http://dx.doi.org/10.1002/macp.200700245

• Hülsmann, Marco; Friedrich, Christoph M.: Comparison of a novel combined ECOC strategy with different multiclass algorithms together with parameter optimization methods. In: Perner, Petra (Hrsg.): Machine learning and data mining in pattern recognition : 5th international conference, MLDM 2007, Leipzig, Germany, July 18-20, 2007 ; proceedings. Berlin [u.a.] : Springer, 2007, S. 17-31 (Lecture notes in computer science 4571 : Lecture notes in artificial intelligence). Institutsveröffentlichung: SCAI: Abteilung: Bioinformatik
  Abstract: In this paper we consider multiclass learning tasks based on Support Vector Machines (SVMs). In this regard, currently used methods are One-Against-All or One-Against-One, but there is much need for improvements in the field of multiclass learning. We developed a novel combination algorithm called Comb-ECOC, which is based on posterior class probabilities. It assigns, according to the Bayesian rule, the respective instance to the class with the highest posterior probability. A problem with the usage of a multiclass method is the proper choice of parameters.
  Many users only take the default parameters of the respective learning algorithms (e.g. the regularization parameter C and the kernel parameter γ). We tested different parameter optimization methods on different learning algorithms and confirmed the better performance of One-Against-One versus One-Against-All, which can be explained by the maximum margin approach of SVMs.
  
  
  Volltext http://dx.doi.org/10.1007/978-3-540-73499-4%5F3 Volltext

• Jacq, Nicolas; Breton, Vincent; Chen, Hsin-Yen; Ho, Li-Yung; Hofmann, Martin; Lee, Hurng-Chun; Legré, Yannick; Lin, Simon C.; Maaß, Astrid; Medernach, Emmannuel; Merelli, Ivan; Milanesi, Luciano; Rastelli, Giulio; Reichstadt, Matthieu; Salzemann, Jean; Schwichtenberg, Horst; Sridhar, Mahendrakar; Kasam, Vinod; Wu, Ying-Ta; Zimmermann, Marc: Grid-Enabled High Throughput Virtual Screening. In: Dubitzky, Werner (Hrsg.) u.a.: Distributed, high-performance and Grid computing in computational biology : international workshop, GCCB 2006, Eilat, Israel, January 2007. Berlin [u.a.] : Springer, 2007, S. 45-59 (Lecture notes in computer science 4360 : Lecture notes in bioinformatics). Institutsveröffentlichung: SCAI http://dx.doi.org/10.1007/978-3-540-69968-2%5F5 Volltext

• Jacq, Nicolas; Breton, Vincent; Chen, Hsin-Yen; Ho, Li-Yung; Hofmann, Martin; Kasam, Vinod; Lee, Hurng-Chun; Legré, Yannick; Lin, Simon C.; Maaß, Astrid; Medernach, Emmanuel; Merelli, Ivan; Milanesi, Luciano; Rastelli, Giulio; Reichstadt, Matthieu; Salzemann, Jean; Schwichtenberg, Horst; Wu, Ying-Ta; Zimmermann, Marc: Virtual screening on large scale grids. In: Parallel computing 33 (2007), 4/5, S. 289-301 Institutsveröffentlichung: SCAI
  Abstract: Large scale grids for in silico drug discovery open opportunities of particular interest to neglected and emerging diseases. In 2005 and 2006, we have been able to deploy large scale virtual docking within the framework of the WISDOM initiative against malaria and avian influenza requiring about 100 years of CPU on the EGEE, Auvergrid and TWGrid infrastructures. These achievements demonstrated the relevance of large scale grids for the virtual screening by molecular docking. This also allowed evaluating the performances of the grid infrastructures and to identify specific issues raised by large scale deployment. (C) 2007 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.parco.2007.02.010

• Jacq, Nicolas (Hrsg.); Müller, Henning (Hrsg.); Blanquer, Ignacio (Hrsg.); Legré, Yannick (Hrsg.); Breton, Vincent (Hrsg.); Hausser, Dominique (Hrsg.); Hernández, Vicente (Hrsg.); Solomonides, Tony (Hrsg.); Hofmann-Apitius, Martin (Hrsg.): From Genes to Personalized HealthCare: Grid Solutions for the Life Sciences - Proceedings of HealthGrid 2007. Amsterdam [u.a.] : IOS Press, 2007 (Studies in health technology and informatics; 126) Institutsveröffentlichung: SCAI: Abteilung: BIO

• Kasam, Vinod; Zimmermann, Marc; Maaß, Astrid; Schwichtenberg, Horst; Wolf, Antje; Jacq, Nicolas; Breton, Vincent; Hofmann-Apitius, Martin: Design of New Plasmepsin Inhibitors : a Virtual High Throughput Screening Approach on the EGEE Grid. In: Journal of chemical information and modeling 47 (2007), 5, S. 1818-1828 Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Though different species of the genus Plasmodium may be responsible for malaria, the variant caused by P. falciparum is often very dangerous and even fatal if untreated. Hemoglobin degradation is one of the key metabolic processes for the survival of the Plasmodium parasite in its host. Plasmepsins, a family of aspartic proteases encoded by the Plasmodium genome, play a prominent role in host hemoglobin cleavage. In this paper we demonstrate the use of virtual screening, in particular molecular docking, employed at a very large scale to identify novel inhibitors for plasmepsins II and IV. A large grid infrastructure, the EGEE grid, was used to address the problem of large computation resources required for docking hundreds of thousands of chemical compounds on different plasmepsin targets of R. falciparum. A large compound library of about I million chemical compounds was docked on 5 different targets of plasmepsins using two different docking software, namely FlexX and AutoDock. Several strategies were employed to analyze the results of this virtual screening approach including docking scores, ideal binding modes, and interactions to key residues of the protein. Three different classes of structures with thiourea, diphenylurea, and guanidino scaffolds were identified to be promising hits. While the identification of diphenylurea compounds is in accordance with the literature and thus provides a sort of "positive control", the identification of novel compounds with a guanidino scaffold proves that high throughput docking,can be effectively used to identify novel potential inhibitors of P. falciparum plasmepsins. Thus, with the work presented here, we do not only demonstrate the relevance of computational grids in drug discovery but. also identify several promising small molecules which have the potential to serve as candidate inhibitors for P. falciparum plasmepsins. With the use of the EGEE grid infrastructure for the virtual screening campaign against the malaria causing parasite P. falciparum we have demonstrated that resource sharing on an eScience infrastructure such as EGEE provides a new model for doing collaborative research to fight diseases of the poor. http://dx.doi.org/10.1021/ci600451t

• Klie, Hector; Wheeler, Mary Fanett; Clees, Tanja; Stüben, Klaus: Deflation AMG Solvers for Highly Ill-Conditioned Reservoir Simulation Problems. In: Society of Petroleum Engineers United States: SPE Reservoir Simulation Symposium 2007 : February 26 -28, 2007, Houston, Texas, USA. SPE, 2007 Institutsveröffentlichung: SCAI: Abteilung: NUSO.SAMG
  Abstract: In recent years, deflation methods have received increasingly particular attention as a means to improving the convergence of linear iterative solvers. This is due to the fact that deflation operators provide a way to remove the negative effect that extreme (usually small) eigenvalues have on the convergence of Krylov iterative methods for solving general symmetric and non-symmetric systems. In this work, we use deflation methods to extend the capabilities of algebraic multigrid (AMG) for handling highly non-symmetric and indefinite problems, such as those arising in fully implicit formulations of multiphase flow in porous media. The idea is to ensure that components of the solution that remain unresolved by AMG (due to the coupling of roughness and indefiniteness introduced by different block coefficients) are removed from the problem. This translates to a constraint to the AMG iteration matrix spectrum within the unit circle to achieve convergence. This approach interweaves AMG (V, W or V-W) cycles with deflation steps that are computable either from the underlying Krylov basis produced by the GMRES accelerator (Krylov-based deflation) or from the reservoir decomposition given by high property contrasts (domain-based deflation). This work represents an efficient extension to the Generalized Global Basis (GGB) method that was recently proposed for the solution of the elastic wave equation with geometric multigrid and an out-of-core computation of eigenvalues. Hence, the present approach offers the possibility of applying AMG to more general large-scale reservoir settings without further modifications to the AMG implementation or algebraic manipulation of the linear system (as suggested by two-stage preconditioning methods). Promising results are supported by a suite of numerical experiments with extreme permeability contrasts.

• Klinger, Roman; Rudolph, Günter: Automatic Composition of Music with Methods of Computational Intelligence. In: WSEAS transactions on information science and applications 4 (2007), 3, S. 508-515 Institutsveröffentlichung: SCAI

• Klinger, Roman; Tomanek, Katrin: Classical probabilistic models and conditional random fields. Dortmund : Technische Universität, 2007 (Algorithm engineering report) Schlagwörter: Conditional Random Fields; Graphical Models; Probability Theory; Machine Learning; Text Mining; Maximum Entropy; Relational Learning Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

• Klinger, Roman; Furlong, Laura I.; Friedrich, Christoph M.; Mevissen, Heinz-Theodor; Fluck, Juliane; Sanz, Ferran; Hofmann-Apitius, Martin: Identifying gene specific variants in biomedical text. In: Journal of bioinformatics and computational biology 5 (2007), 6, S. 1277-1296 Institutsveröffentlichung: SCAI: Abteilung: Bioinformatik http://dx.doi.org/10.1142/S0219720007003156

• Klinger, Roman; Friedrich, Christoph M.; Fluck, Juliane; Hofmann-Apitius, Martin: Named Entity Recognition with Combinations of Conditional Random Fields. In: Hirschmann, Lynette (Hrsg.) u.a.: Proceedings of the Second BioCreative Challenge Evaluation Workshop : April 23-25 2007, Madrid, Spain. Madrid, 2007, S. 89-91 Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: The Gene Mention task is a Named Entity Recognition (NER) task for labeling gene and gene product names in biomedical text. To deal with acceptable alternatives additionally to the gold standard, we use combinations of Conditional Random Fields (CRF) together with a normalizing tagger. This process is followed by a postprocessing step including an acronym disambiguation based on Latent Semantic Analysis (LSA). For robust model selection we apply 50-fold Bootstrapping to obtain an average F-Score of 84.58 % on the trainingset and 86.33 % on the test set.

• Kolárik, Corinna; Hofmann-Apitius, Martin; Zimmermann, Marc; Fluck, Juliane: Identification of new drug classification terms in textual resources. In: Bioinformatics 23 (2007), 13, i264-i272 Institutsveröffentlichung: SCAI: Abteilung: Bioinformatik
  Abstract: Knowledge about biological effects of small molecules helps in the understanding of biological processes and supports the development of new therapeutic agents. DrugBank is a high quality database providing such information about drugs that contains annotation of drug effects and classification of therapeutic effects. However, to broaden the scope of such a database in classifying and annotating drugs, systems for automatic extraction of classification terms and the corresponding annotation of drugs are needed. We have developed an approach for the identification of new terms used in unstructured text that provide information about drug properties. It is based on the identification and extraction of phrases corresponding to lexico-syntactic patterns - so-called Hearst patterns that contain drug names and directly related drug annotation terms. Such phrases could be identified with a high performance in DrugBank text (0.89 F-score) and in Medline abstracts (0.83 F-score). In comparison to DrugBank annotation terminology, a huge amount of new drug annotation terms could be found. The evaluation of terms extracted from Medline showed that 29S53% of them are new valid drug property terms. They could be assigned to existing and new drug property classes not provided by the DrugBank drug annotation. We come to the conclusion that our system can support database content update by providing additionally drug descriptions of pharmacological effects not yet found in databases like DrugBank. Moreover, we propose that automatic normalization of terms improves the annotation and the retrieval of relevant database entries. http://dx.doi.org/doi:10.1093/bioinformatics/btm196

• Krämer-Fuhrmann, Ottmar: RCE and SESIS - Service-Oriented Integration Environment for Collaborative Engineering. In: ERCIM News (2007), 70, S. 30-31 Institutsveröffentlichung: SCAI: Abteilung: SIAN
  Abstract: The 'Reconfigurable Computing Environment' (RCE) is a service-oriented software infrastructure for managing collaborative engineering processes.
  It hides the complexity of heterogeneous and distributed IT systems behind common user interfaces and thus enforces security in the access of data and services. RCE is easily adapted to different application domains: recent work has seen two German ship-building companies build the Ship Design and Simulation System (SESIS) on top of RCE. RCE was jointly developed by the Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) in Sankt Augustin and the German Aerospace Center DLR in Cologne. Volltext

• Kumpf, Kai; Mevissen, Theo; Wäldrich, Oliver; Ziegler, Wolfgang; Ginzel, Sebastian; Weuffel, Thomas: Multi-Cluster Text Mining on the Grid using the D-Grid UNICORE environment. In: German e-Science Conference 2007 : GES 2007, 2. - 4. Mai 2007, Baden-Baden. 2007 Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Text mining is inherently more computation-intensive than information retrieval on pre-structured data and requires transfer and filtering of huge amounts of data. Grid environments provide a suitable infrastructure for accomplishing these tasks.
  We present the mapping and implementation of a standard text mining (TM) workflow for analysis of biomedical text data from PubMed to a D-Grid UNICORE environment with multiple PC-clusters. We discuss the gain in applicability, the open issues of our solution and possible future enhancements. Volltext

• Kumpf, Kai; Mevissen, Theo; Wäldrich, Oliver; Ziegler, Wolfgang; Ginzel, Sebastian; Weuffel, Thomas; Wieder, Philipp; CoreGrid - European Research Network on Foundations, Software Infrastructures and Applications for Large Scale Distributed, GRID and Peer-to-Peer Technologies; Institute on Resource Management and Scheduling: Multi-Cluster Text Mining on the Grid using the D-Grid UNICORE environment. CoreGrid, 2007 (CoreGrid technical report; TR-0109) Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

• Missier, Paolo; Wieder, Philipp; Ziegler, Wolfgang: Semantic Support for Meta-scheduling in Grids. In: Talia, Domenico (Hrsg.) u.a.: Knowledge and Data Management in Grids. New York, NY [u.a.] : Springer, 2007, S. 169-183 (CoreGrid series 3). Schlagwörter: resource management; advance reservation; meta-scheduling; semantic model; Grid Scheduling Ontology Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Co-ordinated usage of resources in a Grid environment is a challenging task impeded by the nature of resource usage and provision: Resources Co-ordinated usage of resources in a Grid environment is a challenging task impeded by the nature of resource usage and provision: Resources reside in different geographic locations, are managed by different organisations, and are by no means accessible via standardised interfaces, protocols or commands. These prerequisites have to be taken into account in order to provide solutions in the area of Grid scheduling and resource management.
  In this document we propose the employment of a semantic model for Grid scheduling. The Grid Scheduling Ontology describes the capabilities and state of a scheduler, providing a machine-processable and interoperable model for the integration of local schedulers into Grid resource management. Along with the model we present a meta-scheduling architecture based on the VIOLA Meta-Scheduling Service that uses ontology modelling and reasoning capabilities of OWL to provide semantic support for meta-scheduling in Grids.
  http://dx.doi.org/10.1007/978-0-387-37831-2%5F11

• Pichot, Antoine; Wieder, Philipp; Ziegler, Wolfgang; Wäldrich, Oliver; CoreGrid - European Research Network on Foundations, Software Infrastructures and Applications for Large Scale Distributed, GRID and Peer-to-Peer Technologies; Institute on Resource Management and Scheduling: Dynamic SLA-negotiation based on WS-Agreement. CoreGrid, 2007 (CoreGrid technical report; TR-0082) Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

• Raoult, Baudouin; Thole, Clemens-August; Gärtel-Zafiris, Ute: Grid technology makes weather forecasts without boundaties a reality. In: ERCIM News (2007), 70, S. 58-59 Institutsveröffentlichung: SCAI Volltext Externer Link

• Rasheed, Hassan; Gruber, Ralf; Keller, Vincent; Wäldrich, Oliver; Ziegler, Wolfgang; Wieder, Philipp; Kuonen, Pierre; Sawley, Marie-Christine; Maffioletti, Sergio; Kunszt, Peter; CoreGrid - European Research Network on Foundations, Software Infrastructures and Applications for Large Scale Distributed, GRID and Peer-to-Peer Technologies; Institute on Resource Management and Scheduling: IANOS: An Intelligent Application Oriented Scheduling Middleware for a HPC Grid. CoreGrid, 2007 (CoreGrid technical report; TR-0110) Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

• Rümpler, Christian; Reichert, Frank; Berger, Frank; Stammberger, Hartwig; Terhoeven, Peter: Simulation and verification of the arc behaviour in quenching chambers with splitter plates. In: XVIIth Symposium on Physics of Switching Arc. Brno : Letohrad, 2007, S. 181-184 (XVIIth Symposium on Physics of Switching Arc 1). Institutsveröffentlichung: SCAI: Abteilung: SIAN
  Abstract: The first part of the paper deals with the experimental investigation of the arc behaviour in quenching chambers of low-voltage devices with different splitter plate arrangements. Besides the measurement of the electrical quantities current and arc voltage, the pressure was recorded at different positions in the chamber wall. For the characterisation of the arc behaviour optical records were taken with a high speed video camera and with a high resolution digital imaging system simultaneously.
  The influence of several parameters such as the shape, number and material of splitter plates on arc movement and arc voltage increase has been investigated.
  In the second part of the paper, the numerical modelling of the arcing processes is presented. In the simulations a non-grey P-1 radiation model is applied to a three dimensional configuration. Details of the radiation model are presented in another paper of this conference. The comparison of results obtained with this model and with assumptions for the radiative transfer given in literature shows that in order to obtain good results it is very important to use a model for the radiative transfer close to reality. Additionally some numerical results concerning the arc splitting process are presented.
  

• Rümpler, Christian; Zacharias, Albert: Simulation of the switching arc for a motor protective circuit breaker. In: Wolf, Klaus Dieter (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 8TH MpCCI User Forum 2007 : February 13 and 14, 2007, Sankt Augustin ; proceedings. Sankt Augustin : Fraunhofer SCAI, 2007, S. 62-69 Institutsveröffentlichung: SCAI: Abteilung: SIAN

• Rümpler, Christian; Reichert, Frank; Stammberger, Hartwig; Terhoeven, Peter; Berger, Frank: Simulation und Verifikation des Lichtbogenlaufverhaltens in Löschkammerkonstruktionen. In: Schöpf, Thomas (Hrsg.); Energietechnische Gesellschaft Deutschland / Fachbereich Kontaktverhalten und Schalten: Kontaktverhalten und Schalten : 19. Fachtagung Albert-Keil-Kontaktseminar vom 26. bis 28. September 2007 an der Universität Karlsruhe. Berlin, Offenbach : VDE-Verlag, 2007, S. 121-130 (VDE-Fachbericht 63). Institutsveröffentlichung: SCAI: Abteilung: SIAN
  Abstract: Die Vorhersage des Lichtbogenverhaltens in Niederspannungs-Schaltgeräten mittels numerischer Simulationen ist im Begriff, mittels verfeinerter physikalischer Modelle und steigender Berechnungskapazitäten ein wichtiges Werkzeug in der Schaltgeräteentwicklung zu werden. In früheren Veröffentlichungen wurden dazu Modelle für die Simulation des Lichtbogens sowie experimentelle Untersuchungen zur Verifikation des Berechnungsmodells vorgestellt. In diesem Beitrag werden nun Verbesserungen des Modells aufgezeigt und die experimentellen Untersuchungen systematisiert.
  Der Energieumsatz infolge der Strahlung ist ein großer Anteil an der Gesamtenergiebilanz. Daher wird ein verbessertes 6-Band P1-Modell für nicht graue Strahlung vorgestellt. Weiterhin hat der durch den Abbrand von Kontaktwerkstoffen eingebrachte Metalldampf einen Einfluss auf den Schaltvorgang. Ansätze zur Modellierung werden vorgestellt, Einflussparameter analysiert und mit experimentellen Ergebnissen verglichen.

• Schwarz, Fritz: Algorithmic Lie theory for solving ordinary differential equations. Boca Raton, Fla. [u.a.] : Chapman & Hall/CRC, 2007 (Pure and applied mathematics; 291) Schlagwörter: Lie Symmetries; Differential Equations; Computer Algebra Institutsveröffentlichung: SCAI: Abteilung: INA
  Abstract: Despite the fact that Sophus Lie's theory was virtually the only systematic method for solving nonlinear ordinary differential equations (ODEs), it was rarely used for practical problems because of the massive amount of calculations involved. But with the advent of computer algebra programs, it became possible to apply Lie theory to concrete problems. Taking this approach, Algorithmic Lie Theory for Solving Ordinary Differential Equations serves as a valuable introduction for solving differential equations using Lie's theory and related results.
  After an introductory chapter, the book provides the mathematical foundation of linear differential equations, covering Loewy's theory and Janet bases. The following chapters present results from the theory of continuous groups of a 2-D manifold and discuss the close relation between Lie's symmetry analysis and the equivalence problem. The core chapters of the book identify the symmetry classes to which quasilinear equations of order two or three belong and transform these equations to canonical form. The final chapters solve the canonical equations and produce the general solutions whenever possible as well as provide concluding remarks. The appendices contain solutions to selected exercises, useful formulae, properties of ideals of monomials, Loewy decompositions, symmetries for equations from Kamke's collection, and a brief description of the software system ALLTYPES for solving concrete algebraic problems.

• Schwarz, Fritz; Grigoriev, Dima: Loewy and primary decomposition of 3D-modules. In: Advances in applied mathematics 38 (2007), 4, S. 526-541 Institutsveröffentlichung: SCAI: Abteilung: INA Volltext http://dx.doi.org/10.1016/j.aam.2005.12.004

• Seidel, Jan; Wäldrich, Oliver; Ziegler, Wolfgang; Wieder, Philipp; Yahyapour, Ramin; CoreGrid - European Research Network on Foundations, Software Infrastructures and Applications for Large Scale Distributed, GRID and Peer-to-Peer Technologies; Institute on Resource Management and Scheduling: Using SLA for resource management and scheduling - a survey. CoreGrid, 2007 (CoreGrid technical report; TR-0096) Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

• Spiess, Holger; Bayrasy, Pacal: How to create your own code adapter. In: Wolf, Klaus Dieter (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 8TH MpCCI User Forum 2007 : February 13 and 14, 2007, Sankt Augustin ; proceedings. Sankt Augustin : Fraunhofer SCAI, 2007, S. 42-45 Institutsveröffentlichung: SCAI

• Stüben, Klaus; Clees, Tanja; Klie, Hector; Lou, Bo; Wheeler, Mary Fanett: Algebraic multigrid methods (AMG) for the efficient solution of fully implicit formulations in reservoir simulation. In: Society of Petroleum Engineers United States: SPE Reservoir Simulation Symposium 2007 : February 26 -28, 2007, Houston, Texas, USA. SPE, 2007 Institutsveröffentlichung: SCAI: Abteilung: NUSO.SAMG
  Abstract: A primary challenge for a new generation of reservoir simulators is the accurate description of multiphase flow in highly heterogeneous media and very complex geometries. However, many initiatives in this direction have encountered difficulties in that current solver technology is still insufficient to account for the increasing complexity of coupled linear systems arising in fully implicit formulations. In this respect, a few works have made particular progress in partially exploiting the physics of the problem in the form of two-stage preconditioners.
  
  Two-stage preconditioners are based on the idea that coupled system solutions are mainly determined by the solution of their elliptic components (i.e., pressure). Thus, the procedure consists of extracting and accurately solving pressure subsystems. Residuals associated with this solution are corrected with an additional preconditioning step that recovers part of the global information contained in the original system.
  
  Optimized and highly complex hierarchical methods such as algebraic multigrid (AMG) offer an efficient alternative for solving linear systems that show a \"discretely elliptic\" nature. When applicable, the major advantage of AMG is its numerical scalability; that is, the numerical work required to solve a given type of matrix problem grows only linearly with the number of variables. Consequently, interest in incorporating AMG methods as basic linear solvers in industrial oil reservoir simulation codes has been steadily increasing for the solution of pressure blocks.
  
  Generally, however, the preconditioner influences the properties of the pressure block to some extent by performing certain algebraic manipulations. Often, the modified pressure blocks are "less favorable"
  for an efficient treatment by AMG. In this work, we discuss strategies for solving the fully implicit systems that preserve (or generate) the desired ellipticity property required by AMG methods. Additionally, we introduce an iterative coupling scheme as an alternative to fully implicit formulations that is faster and also amenable for AMG implementations.
  Hence, we demonstrate that our AMG implementation can be applied to efficiently deal with the mixed elliptic-hyperbolic character of these problems. Numerical experiments reveal that the proposed methodology is promising for solving large-scale, complex reservoir problems.

• Thole, Clemens-August; Nikitina, Lialia; Nikitin, Igor; Steffes-lai, Daniela; Roel, Kersten; Bruns, Jürgen: Constrained optimization with DesParO. In: 2007 Conference 'Virtual Product Development (VPD) in Automotive Engineering' : March 21st-22nd, 2007, Lake Chiemsee/Munich, Germany. PayerConsulting, 2007 Institutsveröffentlichung: SCAI: Abteilung: NUSO
  Abstract: DesParO is a unique system for Design Parameters Optimization, providing the user with complete control of optimization process. Unlike existing automated optimization tools, DesParO allows the user to explore interactively the whole space of design variables and to find the optimal region with respect to multiple design objectives. DesParO provides the user with a global view on the design space, reveals a full set of alternative solutions
  and allows the user to select truly optimal design. Consequently, DesParO is free of common drawbacks inherent to automated optimization tools, such as a solution stuck in a local optimum typical for differential methods or exhaustive numerical experimentation of Monte Carlo alike strategies. In addition to the convenient exploration capabilities, DesParO offers the following unique features. - robust tolerance prediction: DesParO predicts not only the value of the design objective, but also the tolerance limits on the objective. For noisy objectives this allows to satisfy constraints in a safe manner, including the tolerance, and to obtain the robust optimal design.
  - global correlation analysis: DesParO automatically recognizes a pattern of interdependencies between the optimization criteria and design variables and represents it as an easy-to-read color coded diagram. A diagram indicates most influencing design variables, most sensitive optimization criteria and shows also a sign of dependency: increase, decrease or non-monotony. - interpolation of FEM data: DesParO also provides interpolation of bulky data, such as FEM data files containing the results of numerical simulation, to the user specified values of design variables. This allows to visualize a full solution immediately and to inspect in detail the obtained optimal design. We have applied DesParO for solution of a constrained optimization problem at Volkswagen AG. The problem was to minimize the total mass of the vehicle varying thicknesses of 15 car body components, simultaneously targeting constraints on 11 additional optimization criteria related with safety and comfort
  characteristics. Optimization with DesParO allowed to achieve significant mass reduction keeping all constraints satisfied.

• Thole, Clemens-August; Nikitin, Igor; Nikitina, Lialia; Riepl, Mareike: DesParO: Interactive Environment for Multiobjective Parametric Optimization in Automotive Design. In: Joint EUROPT-OMS Meeting 2007 : 2nd Conference on Optimization Methods & Software and 6th EUROPT Workshop on Advances in Continuous Optimization, July 4-7, 2007, in Prague, Czech Republic. EurOpt, 2007 Schlagwörter: Multiobjective optimization; Pareto fronts; catastrophe theory; automotive design Institutsveröffentlichung: SCAI: Abteilung: NUSO
  Abstract: One of the important tasks in Mechanical Engineering is to increase the safety of the vehicle and decrease its production costs. This task is typically solved by means of Multiobjective Optimization, which formulates the problem as a mapping from the space of design variables to the space of target criteria and tries to find an optimal manifold (Pareto front) in these multidimensional spaces. Pareto front is a hypersurface possessing tradeoff property: none of the criteria can be improved without a simultaneous deterioration of at least one other criterion. In this sense the points on the Pareto front are better than the points outside, but they are equally optimal among each other. Pareto front is an ultimate mathematical answer for the optimization problem where several competing objectives are simultaneously targeted. Finally, one of the points on Pareto front should be selected by an extra users decision. The purpose of multiobjective optimization software is to provide a representative set of points on Pareto front for the users selection. We will show that Pareto fronts are identical with singularities of differentiable mappings, appearing in Thoms catastrophe theory. This theory alows to classify geometrical singularities in terms of differential jets and polynomial ideals, and provides efficient algorithms for detection of Pareto fronts both of convex and of non-convex types in multidimensional optimization problems. We also present DesParO, our system for Multiobjective Parametric Optimization, combining Pareto front detection with non-linear multidimensional interpolation on unstructured grids. Unlike existing automated optimization tools, DesParO allows the user to explore Pareto front interactively. Consequently, DesParO is free of common drawbacks inherent to automated optimization tools, such as a solution stuck in a local optimum typical for derivative based methods or exhaustive numerical experimentation of Monte Carlo alike strategies. Finally, we will demonstrate the application of DesParO for solution of real-life multiobjective problems in automotive design, performed in collaboration with Audi and Volkswagen.

• Thole, Clemens-August; Nikitina, Lialia; Nikitin, Igor: Multiobjective Optimization with DesParO. In: OPTIMUS Worldwide Users Meeting : June 25-26, 2007, Leuven, Belgium ; proceedings. Noesis Solutions, 2007 Institutsveröffentlichung: SCAI: Abteilung: NUSO

• Wäldrich, Oliver; Ziegler, Wolfgang; Papaspyrou, Alexander; Wieder, Philipp; Yahyapour, Ramin; CoreGrid - European Research Network on Foundations, Software Infrastructures and Applications for Large Scale Distributed, GRID and Peer-to-Peer Technologies; Institute on Resource Management and Scheduling: Novel Approaches for Scheduling in D-Grid - Towards an Interoperable Scheduling Framework. CoreGrid, 2007 (CoreGrid technical report; TR-0122) Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

• Weidmann, Ernst-Peter; Bauer, Walter; Maihöfer, Martin; Scholl, Uwe: A new CFD and thermal analysis method based on MpCCI. In: Wolf, Klaus Dieter (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 8TH MpCCI User Forum 2007 : February 13 and 14, 2007, Sankt Augustin ; proceedings. Sankt Augustin : Fraunhofer SCAI, 2007, S. 18-27 Institutsveröffentlichung: SCAI

• Wieder, Philipp; Wäldrich, Oliver; Ziegler, Wolfgang; CoreGrid - European Research Network on Foundations, Software Infrastructures and Applications for Large Scale Distributed, GRID and Peer-to-Peer Technologies; Institute on Resource Management and Scheduling: Advanced Techniques for Scheduling, Reservation and Access Management for Remote Laboratories and Instruments. CoreGrid, 2007 (CoreGrid technical report; TR-0078) Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

• Wieder, Philipp; Wäldrich, Oliver; Yahyapour, Ramin; Ziegler, Wolfgang: Improving workflow execution through SLA-based advance reservation. In: Gorlatch, Sergei (Hrsg.) u.a.: Achievements in European research on Grid systems : CoreGRID Integration Workshop 2006, October 19-20, Krakow, Poland ; selected papers. New York, NY : Springer Science+Business Media, 2007, S. 207-222 (CoreGrid series 6). Schlagwörter: Grid; Service Level Agreement; Workflow; Grid Scheduling; WS-Agreement Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: In SOA-based Grid environments service provider and service consumer usually do not know each other. In order to establish a business relation they must interalia (i) create a trust relationship, and (ii) set up mechanisms to create reliable, veri?able, and, at least in a commercial environment, also audible agreements with respect to the services requested, delivered and consumed. In this paper we will only brie?y address (i) but concentrate on solutions for (ii) based on Service Level Agreements (SLAs). Therefore we will give an overview on the state-of-the-art of SLA usage in Grids, highlight possible obstacles for the deployment of SLAs, and present a detailed example of a service improving the execution of work?ows through the use of WS-Agreement to negotiate advance reservation of resources to execute work?ow components.

• Wolf, Armin; Zimmermann, M.; Hofmann-Apitius, Martin: Alternative to consensus scoring : a new approach toward the qualitative combination of docking algorithms. In: Journal of chemical information and modeling - Online 47 (2007), 3, S. 1036-1044 Institutsveröffentlichung: SCAI: Abteilung: BIO http://dx.doi.org/10.1021/ci6004965

• Wolf, Klaus: News around MpCCI Development and Projects. In: Wolf, Klaus Dieter (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 8TH MpCCI User Forum 2007 : February 13 and 14, 2007, Sankt Augustin ; proceedings. Sankt Augustin : Fraunhofer SCAI, 2007, S. 10-17 Institutsveröffentlichung: SCAI

• Wolf, Klaus Dieter (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 8TH MpCCI User Forum 2007 : February 13 and 14, 2007, Sankt Augustin ; proceedings. Sankt Augustin : Fraunhofer SCAI, 2007 Institutsveröffentlichung: SCAI Volltext

2006

• Ananiadou, Sophia; Fluck, Juliane: Introduction. In: BMC bioinformatics 7 : Supplement 3 (2006), S1, S. 1-3 Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext Externer Link

• Second International Symposium on Semantic Mining in Biomedicine (SMBM) Ananiadou, Sophia (Hrsg.) u.a.: BMC bioinformatics 7 : Supplement 3 (2006), S1 Institutsveröffentlichung: SCAI: Abteilung: BIO http://dx.doi.org/10.1186/1471-2105-7-S3-S1

• Ananiadou, Sophia (Hrsg.); Fluck, Juliane (Hrsg.): Second International Symposium on Semantic Mining in Biomedicine - SMBM 2006 : proceedings of the Second International Symposium on Semantic Mining in Biomedicine Jena, April 9-12, 2006. Aachen : RWTH, 2006 (CEUR workshop proceedings; 177) Institutsveröffentlichung: SCAI Volltext

• Arbona, A.; Benkner, S.; Fingberg, J.; Frangi, A.F.; Hofmann, Martin; Hose, D.R.; Lonsdale, G.; Ruefenacht, D.; Viceconti, M.: Outlook for Grid Service technologies within the @neurIST eHealth environment. In: Hernández, Vicente (Hrsg.) u.a.: Challenges and Opportunities of HealthGrids - Proceedings of Healthgrid 2006. Amsterdam [u.a.] : IOS Press, 2006, S. 401-404 (Studies in health technology and informatics 120). Institutsveröffentlichung: SCAI
  Abstract: The aim of the @neurIST project is to create an IT infrastructure for the management of all processes linked to research, diagnosis and treatment development for complex and multi-factorial diseases. The IT infrastructure will be developed for one such disease, cerebral aneurysm and subarachnoid haemorrhage, but its core technologies will be transferable to meet the needs of other medical areas. Since the IT infrastructure for @neurIST will need to encompass data repositories, computational analysis services and information systems handling multi-scale, multi-modal information at distributed sites, the natural basis for the IT infrastructure is a Grid Service middleware. The project will adopt a service-oriented architecture because it aims to provide a system addressing the needs of medical researchers, clinicians and health care specialists (and their IT providers/systems) and medical supplier/consulting industries.

• Barz, Christoph; Pilz, Markus; Eickermann, Thomas; Kirtchakova, Lidia; Wäldrich, Oliver; Ziegler, Wolfgang; CoreGrid - European Research Network on Foundations, Software Infrastructures and Applications for Large Scale Distributed, GRID and Peer-to-Peer Technologies; Institute on Resource Management and Scheduling: Co-Allocation of Compute and Network Resources in the VIOLA Testbed. CoreGrid, 2006 (CoreGrid technical report; TR-0051) Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

• Barz, Christoph; Eickermann, Thomas; Kirtchakova, Lidia; Pilz, Markus; Wäldrich, Oliver; Ziegler, Wolfgang: Co-Allocation of Compute and Network Resources in the VIOLA-Testbed. In: Melve, I. (Hrsg.): TERENA Networking Conference 2006 : 15.-18.05.2006 in Catania. Bradford : Emerald, 2006, 12 S. (Campus-wide information systems 23.2006,4). Schlagwörter: optical networks; quality of service; advance reservations; co-allocation; service level agreement; bandwidth on demand Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Demanding applications like distributed multi-physics simulations benefit from the combined computational performance and data storage of multiple clusters. A reservation mechanism spanning these clusters ensures the availability of all selected resources. Complex workflows with chronological dependencies are supported.
  This approach addresses network resources the same way as computation and storage resources. A Meta Scheduling Service (MSS) does the orchestration of resources of different administrative domains, based on an advance reservation capability of local resource management systems. The combined reservation of computational, storage and network resources as done in the VIOLA project for UNICORE based Grid applications, allows a user or application driven selection and reservation of network connections with dedicated QoS based on evolving network technologies. Volltext

• Beibei, Han; Friedrich, Christoph M.; Manthey, Rainer; Hofmann-Apitius, Martin: Bayesian Network Modeling for the Prediction of Treatment Outcomes of Intracranial Aneurysms. In: Huson, D. (Hrsg.) u.a.; Center for Bioinformatics Tübingen u.a.: Short papers and poster abstracts of the German Conference on Bioinformatics : GCB 2006, 19.9.2006-22.9.2006 in Tübingen, Germany. 2006, S. 122 Institutsveröffentlichung: SCAI: Abteilung: BIO

• Bierbaum, Boris; Clauss, Carsten; Eickermann, Thomas; Kirtchakova, Lidia; Krechel, Arnold; Springstubbe, Stephan; Wäldrich, Oliver; Ziegler, Wolfgang: Reliable Orchestration of distributed MPI-Applications in a UNICORE-based Grid with MetaMPICH and MetaScheduling. In: Mohr, Bernd (Hrsg.) u.a.: Recent advances in parallel virtual machine and message passing interface : 13th European PVM/MPI User's Group Meeting, Bonn, Germany, September 17-20, 2006 ; proceedings. Berlin [u.a.] : Springer, 2006, S. 174-183 (Lecture notes in computer science 4192). Institutsveröffentlichung: SCAI: Abteilung: BIO http://dx.doi.org/10.1007/11846802%5F29 Volltext

• Bierbaum, Boris; Clauss, Carsten; Eickermann, Thomas; Kirtchakova, Lidia; Krechel, Arnold; Springstubbe, Stephan; Wäldrich, Oliver; Ziegler, Wolfgang; CoreGrid - European Research Network on Foundations, Software Infrastructures and Applications for Large Scale Distributed, GRID and Peer-to-Peer Technologies; Institute on Resource Management and Scheduling: Reliable Orchestration of distributed MPI-Applications in a UNICORE-based Grid with MetaMPICH and MetaScheduling. CoreGrid, 2006 (CoreGrid technical report; TR-0052) Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

• Birkholtz, Lyn-Marie; Bastien, Olivier; Wells, Gordon; Grando, Delphine; Joubert, Fourie; Kasam, Vinod; Zimmermann, Marc; Ortet, Philippe; Jacq, Nicolas; Saïdani, Nadia; Roy, Sylvaine; Hofmann-Apitius, Martin; Breton, Vincent; Louw, Abraham I.; Maréchal, Eric: Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space? In: Malaria journal 5 (2006) Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: The organization and mining of malaria genomic and post-genomic data is important to significantly increase the knowledge of the biology of its causative agents, and is motivated, on a longer term, by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should, therefore, be as reliable and versatile as possible. In this context, five aspects of the organization and mining of malaria genomic and post-genomic data were examined: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes, particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Recent progress towards a grid-enabled chemogenomic knowledge space is discussed. Volltext http://dx.doi.org/10.1186/1475-2875-5-110

• Breton, Vincent; Jacq, Nicolas; Hofmann, Martin: Grid added value to address malaria. In: Institute of Electrical an Electronics Engineers: Proceedings of the Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGRID '06) : Singapore May 16-19, 2006. Washington, DC : IEEE Computer Society Press, 2006, S. 40 Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Through this paper, we call for a distributed, internet-based collaboration to address one of the worst plagues of our present world, malaria. The spirit is a non-proprietary peer-production of informationembedding goods. And we propose to use the grid technology to enable such a world wide "open source" like collaboration. The first step towards this vision has been achieved during the summer on the EGEE grid infrastructure where 46 million ligands were docked for a total amount of 80 CPU years in 6 weeks in the quest for new drugs. http://doi.ieeecomputersociety.org/10.1109/CCGRID.2006.139

• Cristiano, Kevin; Kuonen, Pierre; Gruber, Ralf; Keller, Vincent; Spada, Michela; Tran, Trach-Minh; Maffioletti, Sergio; Nellari, Nello; Sawley, Marie-Christine; Wäldrich, Oliver; Ziegler, Wolfgang; Wieder, Philipp; CoreGrid - European Research Network on Foundations, Software Infrastructures and Applications for Large Scale Distributed, GRID and Peer-to-Peer Technologies; Institute on Resource Management and Scheduling: Integration of ISS into the VIOLA Meta-Scheduling Environment. CoreGrid, 2006 (CoreGrid technical report; TR-0025) Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

• Dehning, Carsten; Holländer, A.; Leventi-Peetz, A.-M.; Silmy, K.: Simulation of a Plasma Enhanced µ-jet-CVD Process. In: NAFEMS International Journal of CFD Case Studies 5 (2006) Institutsveröffentlichung: SCAI: Abteilung: SIAN

• Friedrich, Christoph M.; Revillion, Thomas; Hofmann, Martin; Fluck, Juliane: Biomedical and chemical named entity recognition with conditional random fields: the advantages of dictionary features : presentation held at the second International Symposium on Semantic Mining in Biomedicine, Jena, April 9-12, 2006. Jena, 2006 Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext Volltext Externer Link

• Friedrich, Christoph M.; Zimmermann, Marc; Hofmann, Martin: Grid computing - an opportunity for biomedical and statistical computing : Talk at Statistical Computing 2006. In: Statistical Computing 2006 : 38. Arbeitstagung über Methoden und Werkzeuge der Informatik für die Statistik, 25. - 28.06.2006, Schloss Reisensburg (Günzburg). 2006, S. 5 Institutsveröffentlichung: SCAI: Abteilung: BIO

• Furlong, Laura I.; Dach, Holger; Hofmann-Apitius, Martin; Sanz, Ferran: Towards a development of a text-mining system for genes, sequence variants and phenotypes: integration of OSIRIS with ProMiner. In: University Zaragoza u.a.: 7th Spanish Symposium on Bioinformatics and Computational Biology : JdB '06, Zaragoza, Spain, November 20-22, 2006. Zaragoza, 2006 Institutsveröffentlichung: SCAI: Abteilung: BIO

• Grawe, Johannes; Wolf, Klaus: Multidisciplinary simulation and visualisation with MpCCI and EnSight. In: Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 7th MpCCI User Forum : February 21st and 22nd, 2006, Schloss Birlinghoven, Sankt Augustin, Germany ; proceedings. Sankt Augustin : Fraunhofer SCAI, 2006, S. 66-75 Institutsveröffentlichung: SCAI

• Hensel, Hartmut; Iza-Teran, Rodrigo; Siedow, Norbert: Deterministic model for dose calculation in photon radiotherapy. In: Physics in medicine and biology 51 (2006), 3, S. 675-693 Institutsveröffentlichung: SCAI
  Abstract: We present a model for dose calculation in photon radiotherapy based on deterministic transport equations. The model consists of two coupled equations, one for photon and one for electron transport and an equation for the absorbed dose. No assumptions are made with respect to the geometry or the homogeneity of the irradiated medium, so irradiation of any heterogenous medium can be simulated. To get a mathematically simpler model, approximations to the exact equations are presented which keep the essential physical contents of the exact equations, but which can be solved with less numerical effort. The results of dose calculations for simple examples are presented and discussed. http://dx.doi.org/10.1088/0031-9155/51/3/013

• Jacq, Nicolas; Salzemann, Jean; Legré, Yannick; Reichstadt, Matthieu; Jacq, Florence; Zimmermann, Marc; Maass, Astrid; Sridhar, Mahendrakar; Vinod-Kusam, Kasam; Schwichtenberg, Horst; Hofmann, Martin; Breton, Vincent: Demonstration of in silico docking at a large scale on grid infrastructure. In: Hernández, Vicente (Hrsg.) u.a.: Challenges and Opportunities of HealthGrids - Proceedings of Healthgrid 2006. Amsterdam [u.a.] : IOS Press, 2006, S. 155-157 (Studies in health technology and informatics 120). Institutsveröffentlichung: SCAI: Abteilung: BIO

• Joppich, Wolfgang; Kürschner, M.: MpCCI - a tool for the simulation of coupled applications. In: Concurrency and computation 18 (2006), 2, S. 183-192 Institutsveröffentlichung: SCAI
  Abstract: Many industrial and scientific applications are characterized by the interaction of different disciplines, such as fluid-structure interactions. For the individual disciplines sophisticated and validated solvers exist. This paper describes basic ideas, implementation details and application of MpCCI (mesh-based parallel code coupling interface), a tool for the coupling of different simulation codes. http://dx.doi.org/10.1002/cpe.913

• Karopka, Thomas; Fluck, Juliane; Mevissen, Heinz-Theodor; Glass, Änne: The Autoimmune Disease Database: a dynamically compiled literature-derived database. In: BMC bioinformatics 7 (2006), S. 325 Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Background: Autoimmune diseases are disorders caused by an immune response directed against the body's own organs, tissues and cells. In practice more than 80 clinically distinct diseases, among them systemic lupus erythematosus and rheumatoid arthritis, are classified as autoimmune diseases. Although their etiology is unclear these diseases share certain similarities at the molecular level i.e. susceptibility regions on the chromosomes or the involvement of common genes. To gain an overview of these related diseases it is not feasible to do a literary review but it requires methods of automated analyses of the more than 500,000 Medline documents related to autoimmune disorders. Results: In this paper we present the first version of the Autoimmune Disease Database which to our knowledge is the first comprehensive literature-based database covering all known or suspected autoimmune diseases. This dynamically compiled database allows researchers to link autoimmune diseases to the candidate genes or proteins through the use of named entity recognition which identifies genes/proteins in the corresponding Medline abstracts. The Autoimmune Disease Database covers 103 autoimmune disease concepts. This list was expanded to include synonyms and spelling variants yielding a list of over 1,200 disease names. The current version of the database provides links to 541,690 abstracts and over 5,000 unique genes/proteins. Conclusion: The Autoimmune Disease Database provides the researcher with a tool to navigate potential gene-disease relationships in Medline abstracts in the context of autoimmune diseases.
  Volltext Externer Link http://dx.doi.org/10.1186/1471-2105-7-325

• Keller, Vincent; Gruber, Ralf; Spada, Michaela; Tran, Trach-Minh; Cristiano, Kevin; Kuonen, Pierre; Wieder, Philipp; Ziegler, Wolfgang; Wälderich, Oliver; Maffioletti, Sergio; Sawley, Marie-Christine; Nellari, Nello: Integration of the ISS into the VIOLA Meta-Scheduling. In: Gorlatch, Sergei (Hrsg.) u.a.: Integrated Research in GRID Computing : CoreGRID Integration Workshop 2005, November 28-30, Pisa, Italy. Berlin : Springer US, 2006, S. 203-214 Schlagwörter: Grid; Scheduling; Co-allocation; Resource pre-selection Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: The authors present the integration of the Intelligent (Grid) Scheduling System into the VIOLA meta-scheduling environment which itself is based on the UNICORE Grid software. The goal of the new, integrated environment is to enable the submission of jobs to the Grid system best-suited for the application workflow. For this purpose a cost function is used that exploits information about the type of application, the characteristics of the system architectures, as well as the availabilities of the resources. This document presents an active collaboration between Ecole Polytechnique Fédérale de Lausanne (EPFL), Ecole d'Ingénieurs et d'Architectes (EIF) de Fribourg, Forschungszentrum Jülich, Fraunhofer Institute SCAI, and Swiss National Supercomputing Centre (CSCS). http://dx.doi.org/10.1007/978-0-387-47658-2%5F15

• Klimenko, Stanislav V.; Nikitin, Igor; Nikitina, Lialia: Avango : systema rasrabotki virtualneuch okruschenii. Moskva : Agross, 2006 Institutsveröffentlichung: SCAI: Abteilung: NUSO

• Klinger, Roman; Rudolph, Günter: Evolutionary Composition of Music with Learned Melody Evaluation. In: Mastorakis, Nikos (Hrsg.) u.a.; World Scientific and Engineering Academy and Society: Proceedings of the The 5th WSEAS International Conference on Computational Intelligence, Man-Machine Systems and Cybernetics (CIMMACS '06) : Venice, Italy, November 20-22, 2006. 2006, S. 234-239 Institutsveröffentlichung: SCAI

• Krapp, Michael (Red.): Jahresbericht 2005 / Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI. Sankt Augustin : Fraunhofer SCAI, 2006 (Jahresbericht / Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI) Institutsveröffentlichung: SCAI Volltext

• Kumpf, Kai; Mevissen, Theodor; Wäldrich, Oliver; Weuffel, Thomas; Ziegler, Wolfgang: Text Mining on the Grid. In: Workshop on Grid Technologies for Knowledge-based Industries and Businesses : Helsinki, Finland, November 21-23, 2006 ; proceedings. Helsinki, 2006 Schlagwörter: Text Mining; Workflow; UNICORE Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Text mining is inherently more computation-intensive than information retrieval on pre-structured data and requires transfer and filtering of huge amounts of data. Grid environments provide the infrastructure for accomplishing these tasks. We present the mapping and implementation of a standard text mining (TM) workflow for analysis of biomedical text data from PubMed to a UNICORE Grid environment with multiple PC-clusters. Both the gain in applicability and the open issues of our solution are discussed.

• Ludwig, Heiko; Nakata, Toshiyuki; Wäldrich, Oliver; Wieder, Philipp; Ziegler, Wolfgang: Reliable Orchestration of Resources using WS-Agreement. In: Gerndt, Michael (Hrsg.) u.a.: High performance computing and communications : second international conference, HPCC 2006, Munich, Germany, September 2006 ; proceedings. Berlin [u.a.] : Springer, 2006, S. 753-762 (Lecture notes in computer science 4208). Institutsveröffentlichung: SCAI: Abteilung: BIO http://dx.doi.org/10.1007/11847366%5F78 Volltext

• Ludwig, Heiko; Nakata, Toshiyuki; Wieder, Philipp; Wäldrich, Oliver; Ziegler, Wolfgang; CoreGrid - European Research Network on Foundations, Software Infrastructures and Applications for Large Scale Distributed, GRID and Peer-to-Peer Technologies; Institute on Resource Management and Scheduling: Reliable Orchestration of Resources using WS-Agreement. CoreGrid, 2006 (CoreGrid technical report; TR-0050) Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

• Milke, Jens-Michael; Schiffers, Michael; Ziegler, Wolfgang: Virtuelle Organisationen in Grids : Charakterisierung und Management. In: PIK-Praxis der Informationsverarbeitung und Kommunikation 29 (2006), 3, S. 166-171 Institutsveröffentlichung: SCAI: Abteilung: BIO

• Missier, Paolo; Wieder, Philipp; Ziegler, Wolfgang; CoreGrid - European Research Network on Foundations, Software Infrastructures and Applications for Large Scale Distributed, GRID and Peer-to-Peer Technologies: Semantic Support for Meta-Scheduling in Grids. CoreGrid, 2006 (CoreGrid technical report; TR-0030) Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Co-ordinated usage of resources in a Grid environment is a challenging task impeded by the nature of resource usage and provision: Resources reside in different geographic locations, are managed by different organisations, and are by no means accessible via standardised interfaces, protocols or commands. These prerequisites have to be taken into account in order to provide solutions in the area of Grid scheduling and resource management. In this document we propose the employment of a semantic model for Grid scheduling. The Grid Scheduling Ontology describes the capabilities and state of a scheduler, providing a machine-processable and interoperable model for the integration of local schedulers into Grid resource management. Along with the model we present a metascheduling architecture based on the VIOLA Meta-Scheduling Service that use ontology modelling and reasoning capabilities of OWL to provide semantic support for meta-scheduling in Grids. Volltext

• Rank, Stefan; Schwefel, Hans-Paul: Transient analysis of RED queues : a quantitative analysis of buffer-occupancy fluctuations and relevant time-scales. In: Performance evaluation 63 (2006), 8, S. 725-742 Schlagwörter: Random Early Detection queues; Transient analysis; Buffer occupancy; Mobile networks; Quality of service Institutsveröffentlichung: SCAI
  Abstract: This paper presents an analytic model for the transient behavior of the buffer occupancy in Random Early Detection (RED) queues under temporarily constant input traffic. The model shows that depending on the parameter
  choice, two types of qualitatively different behavior can be observed: (1) attenuated oscillation and (2) exponential convergence. The conditions for the occurrence of this behavior are derived as well as quantitative parameters in particular relaxation times, that allow to quantify the time-scales on which that transient behavior is observed. The model is subsequently applied to investigate an example scenario based on RED queues in a DiffServ QoS concept in which traffic changes are caused by mobility events. http://dx.doi.org/10.1016/j.peva.2005.08.001

• Rümpler, Christian; Reichert, Frank; Stammberger, Hartwig; Terhoeven, Peter; Berger, Frank: Numerical study of the electrical arc movement supported by experiments. In: The 23rd International Conference on Electrical Conference on Electrical Contacts : ICEC 2006, Sendai, Japan, 6-9 June 2006 together with the 6th International Session on Electromechical Devices, IS-EMD 2006 ; proceedings. 2006, S. 22-27 Schlagwörter: arc; low voltage; coupling Institutsveröffentlichung: SCAI: Abteilung: SIAN
  Abstract: The aim of this study is the development of a numerical model for the prediction of the dynamic arc behaviour in low voltage switching devices. Due to the high thermal and mechanical stresses caused by the electric arc between the contacts of the switch the knowledge and prediction of the interactions between fluid dynamics and magnetic field is fundamental for the development of such devices.
  By means of a commercial finite volume code we solve the fluid dynamics problem and a commercial finite element code is used to solve Maxwell\'s equations. The two physical domains are coupled via a coupling interface which is responsible for the data exchange between the programms.
  Numerical investigations based on a parallel electrode configuration are presented and compared to experimental results. Depending on the current level we observe different arc movement behaviour, discontinuous and continuous movement, respectively, which is in fact an alternation from arc root dominated behaviour to electro-dynamically minated behaviour. Consindering these phenomena the numerical and experimental results are compared and show good agreement for the arc voltage and for the arc movement.

• Springstubbe, Stephan: CoreGRID Summer School 2006 : first steps in next generation Grid technologies. In: ERCIM News (2006), 67, S. 4 Institutsveröffentlichung: SCAI Volltext externer Link

• Streit, Achim; Wäldrich, Oliver; Wieder, Philipp; Ziegler, Wolfgang: On Scheduling in UNICORE - Extending the Web Services Agreement based Resource Management Framework. In: Joubert, G.R. (Hrsg.) u.a.; John von Neumann Institute for Computing Jülich: Parallel computing: current & future issues of high-end computing : proceedings of the International Conference ParCo 2005. Jülich : NIC, 2006, S. 57-64 (NIC series 33). Institutsveröffentlichung: SCAI: Abteilung: BIO

• Thole, Clemens-August; Stork, André; Wundrak, Stefan; Nikitina, Lialia: Simulierte Realität in der Crashoptimierung: in 15 Sekunden zu einem neuen Crashergebnis. In: 24th CADFEM Users' Meeting 2006 : International Congress on FEM Technology with 2006 German Ansys Conference, 25. - 27. Oktober 2006, Stuttgart/Fellbach. München, 2006 Institutsveröffentlichung: SCAI: Abteilung: Numerische Software

• Wäldrich, Oliver; Wieder, Philipp; Ziegler, Wolfgang: A Meta-Scheduling Service for Co-allocating Arbitrary Types of Resources. In: Wyrzykowski, Roman (Hrsg.) u.a.: Parallel processing and applied mathematics : 6th international conference, PPAM 2005, Poznan, Poland, September 11-14, 2005, revised selected papers. Berlin [u.a.] : Springer, 2006, S. 782-791 (Lecture notes in computer science 3911). Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: The Grid paradigm implies the sharing of a
  variety of resources across multiple
  administrative domains. In order to execute a
  work-flow using these distributed resources an
  instrument is needed to co-allocate resources by
  reaching agreements with the different local
  scheduling systems involved. Apart from compute
  resources to execute the work-flow the
  co-ordinated usage of other resource types must
  be also guaranteed, as there are for example a
  network connectivity with dedicated QoS
  parameters or a visualisation device. We present
  a Web Service-based MetaScheduling Service which
  allows to negotiate a common time slot with
  local resource management systems to enable the
  execution of a distributed work-flow. The
  successful negotiation process results in a
  formal agreement based on the WS-Agreement
  recommendation that is currently specified by
  the GRAAP working group of the Global Grid Forum.
  As a use case we demonstrate the integration of
  this MetaScheduling Service into the UNICORE
  middleware. http://dx.doi.org/10.1007/11752578%5F94 Volltext

• Weidmann, Ernst-Peter; Scholl, U.; Bauer, W.; Maihöfer, Martin; Wiedemann, J.: A new CFD and thermal analysis method based on MpCCI. In: International Federation of Automobile Techniques Engineers: FISITA 2006 World Automotive Congress : 22 - 27 October, Yokohama, Japan. Yokohama, 2006 Institutsveröffentlichung: SCAI

• Wieder, Philipp; Wäldrich, Oliver; Ziegler, Wolfgang: Advanced Techniques for Scheduling, Reservation, and Access Management for Remote Laboratories. In: Second IEEE International Conference on e-Science and Grid Computing (e-Science'06). Los Alamitos, Calif. : IEEE Computer Society, 2006, S. 128 Institutsveröffentlichung: SCAI: Abteilung: BIO

• Wieder, Philipp; Wäldrich, Oliver; Yahyapour, Ramin; Ziegler, Wolfgang: Improving Workflow execution through SLA-based Advance Reservation. In: Integrated Research in Grid Computing : CoreGRID Integration Workshop, Krakow, October 19-20, 2006. 2006, S. 333-344 Schlagwörter: Grid; Scheduling; Workflow; Resource reservation Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: In SOA-based Grid environments service provider and service consumer usually do not know each other. In order to establish a business relation they must inter alia (i) create a trust relationship, and (ii) set up mechanisms to create reliable, verifiable, and, at least in a commercial environment, also audible agreements with respect to the services requested, delivered and consumed. In this paper we will only briefly address (i) but concentrate on solutions for (ii) based on Service Level Agreements (SLAs). Therefore we will give an overview on the state-of-the-art of SLA usage in Grids, highlight possible obstacles for the deployment of SLAs, and present a detailed example of a service improving the execution of workflows through the use of WS-Agreement to negotiate advance reservation of resources to execute workflow components.

• Wieder, Philipp; Yahyapour, Ramin; Wäldrich, Oliver; Ziegler, Wolfgang; CoreGrid - European Research Network on Foundations, Software Infrastructures and Applications for Large Scale Distributed, GRID and Peer-to-Peer Technologies; Institute on Resource Management and Scheduling: Improving Workflow Execution through SLA-based Advance Reservation. CoreGrid, 2006 (CoreGrid technical report; TR-0053) Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

• Wienands, Roman: Coarse grid approximation governed by local. In: Wesseling, P. (Hrsg.) u.a.: Proceedings ECCOMAS CFD 2006 : European Conference on Computational Fluid Dynamics, Egmond aan Zee, The Netherlands, September 5-8, 2006. Delft : Technische Universiteit, 2006 Institutsveröffentlichung: SCAI

• Wienss, Christian; Nikitin, Igor; Goebbels, Gernot; Troche, Klaus; Göbel, Martin; Nikitina, Lialia; Müller, Stefan: Sceptre: an infrared laser tracking system for virtual environments. In: Association for Computing Machinery: VRST '06 : ACM Symposium on Virtual Reality Software & Technology, November 1-3, 2006, Limassol, Cyprus ; proceedings. New York, NY : ACM Press, 2006, S. 45-50 Institutsveröffentlichung: SCAI http://dx.doi.org/10.1145/1180495.1180506

• Wolf, Klaus: MpCCI development and business issues. In: Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 7th MpCCI User Forum : February 21st and 22nd, 2006, Schloss Birlinghoven, Sankt Augustin, Germany ; proceedings. Sankt Augustin : Fraunhofer SCAI, 2006, S. 10-21 Institutsveröffentlichung: SCAI

• Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 7th MpCCI User Forum : February 21st and 22nd, 2006, Schloss Birlinghoven, Sankt Augustin, Germany ; proceedings. Sankt Augustin : Fraunhofer SCAI, 2006 Institutsveröffentlichung: SCAI

• Ziegler, Wolfgang; Wieder, Philipp: Bringing Knowledge to Middleware - Grid Scheduling Ontology. In: Getov, Vladimir (Hrsg.) u.a.: Future generation grids : proceedings of the Workshop on Future Generation Grids, November 1-5, 2004, Dagstuhl, Germany. New York, NY [u.a.] : Springer, 2006, S. 47-59 Schlagwörter: Scheduling; Ontologie; Ressource Management; OWL Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: The Grid paradigm implies the sharing of a variety
  of resources across multiple administrative
  domains. Assuming that such an environment is
  highly dynamic, it is essential to abstract
  potential drawbacks away from resource users
  and resource providers. One crucial aspect in
  designing and operating Grids to gain the
  respective abstraction is the provision of a
  sophisticated scheduling and resource management
  framework. Experience shows that scheduling a
  single resource like an HPC system is already a
  challenge, but the co-ordinated scheduling of
  multiple resources to automatically process a
  complex work flow is impossible if the
  capabilities of resources are not a priori known.
  We propose to make scheduling-specific parts of
  such knowledge exploitable by introducing a
  scheduling domain ontology. This ontology provides
  a common semantic understanding to be shared
  between the components involved in the scheduling
  process. By agreeing upon and integrating such an
  ontology we increase the automation level and
  make usage and administration of Grids easier.

• Ziegler, Wolfgang; Eickermann, Thomas; Moll, Wolfgang; Hommes, Ferdinand; Clauss, Carsten: SLA based resource orchestration using UNICORE : Poster at ISC 2006, Juni 2006, Dresden. 2006 Institutsveröffentlichung: SCAI: Abteilung: BIO Institutsveröffentlichung: IAIS Volltext

• Zitzmann, Martin-Ludwig; Grillmair, Robert; Clees, Tanja; Weigel, Robert: Hybrid solver strategies in automotive EMC simulation. In: Proceedings of 17th International Zurich Symposium on Electromagnetic Compatibility (EMC-Zurich) : Singapore, February 27 - March 3, 2006. New York, NY : IEEE, 2006, S. 340-343 Institutsveröffentlichung: SCAI: Abteilung: NUSO.SAMG
  Abstract: Switching operations in integrated circuits are often the reason for electromagnetic disturbances which can spread over the whole system. This is especially important for automotive applications where many control systems are connected together via cable harnesses. Although model order reduction techniques help to reduce the computational effort resulting from realistic automotive simulation problems suitable solver strategies are indispensable. Their efficiency highly depends on the matrix properties which are directly affected by the kind of modeling and simulation approach. In this paper it is shown that hybrid solver strategies are most advantageous for flexible EM simulation. Analysis of the matrix properties helps to identify the most appropriate solver.

• Zitzmann, Martin-Ludwig; Clees, Tanja; Weigel, Robert: Iterative methods for reluctance based {PEEC} models. In: Proceedings of 17th International Zurich Symposium on Electromagnetic Compatibility (EMC-Zurich) : Singapore, February 27 - March 3, 2006. New York, NY : IEEE, 2006, S. 81-84 Institutsveröffentlichung: SCAI: Abteilung: NUSO.SAMG
  Abstract: Switching operations in integrated circuits are often the reason for electromagnetic disturbances which can spread over the whole system. This is especially important for automotive applications where many control systems are connected together via cable harnesses. Although model order reduction techniques help to reduce the computational effort resulting from realistic automotive simulation problems suitable solver strategies are indispensable. Their efficiency highly depends on the matrix properties which are directly affected by the kind of modeling and simulation approach. In this paper it is shown that hybrid solver strategies are most advantageous for flexible EM simulation. Analysis of the matrix properties helps to identify the most appropriate solver.

2005

• Brandes, Thomas; Schwamborn, Helmut; Gerndt, Michael; Jeitner, Jürgen; Kereku, Edmond; Schulz, Martin; Brunst, Holger; Nagel, Wolfgang; Neumann, Reinhard; Müller-Pfefferkorn, Ralph; Trenkler, Bernd; Karl, Wolfgang; Tao, Jie; Hoppe, Hans-Christian: Monitoring cache behavior on parallel SMP architectures and related programming tools. In: Future generation computer systems 21 (2005), 8, S. 1298-1311 Schlagwörter: Hardware Cache Monitoring; Performance Analysis; Cache Optimizations; Parallel Programming Tools Institutsveröffentlichung: SCAI: Abteilung: NUSO
  Abstract: This paper describes the ideas and developments of the project EP-CACHE.
  Within this project new methods and tools are developed to improve the analysis and the optimization of programs
  for cache architectures, especially for SMP clusters. The tool set comprises the semi-automatic instrumentation of user programs, the monitoring of the cache behavior, the visualization of the measured data, and optimization techniques for improving the user program for better cache usage.
  As current hardware performance counters do not give sufficient user relevant information, new hardware monitors are designed that provide more detailed information about the cache utilization related to the data structures and code blocks in the user program.
  The expense of the hardware and software realization will be assessed to minimize the risk of a real implementation of the investigated monitors. The usefulness of the hardware monitors is evaluated by a cache simulator. http://dx.doi.org/10.1016/j.future.2004.09.005

• Dach, Holger; Kumpf, Kai; Hofmann, Martin; Manthey, Rainer; Fluck, Juliane: A new information system to maintain and analyse biochemical interaction networks : Poster. Hamburg, 2005 Institutsveröffentlichung: SCAI: Abteilung: Bioinformatik

• Fluck, Juliane; Zimmermann, Marc; Kurapkat, Günther; Hofmann, Martin: Information extraction technologies for the life science industry. In: Drug discovery today 2 (2005), 3, S. 217-224 Institutsveröffentlichung: SCAI: Abteilung: Bioinformatik http://dx.doi.org/10.1016/j.ddtec.2005.08.013

• Fluck, Juliane; Hofmann, Martin; Hahn, Udo; Wermter, Joachim; Schulz, Stefan: Text mining in den Life Sciences : Perspektiven der automatischen Informationsextraktion aus biomedizinischen Fachtexten. In: Deutsche Zeitschrift für klinische Forschung 5/6 (2005), S. 20-26 Institutsveröffentlichung: SCAI: Abteilung: BIO

• Fluck, Juliane; Deneke, Hartwig; Gieger, Christian: Text mining in life sciences. In: Zanasi, Alessandro (Hrsg.): Text Mining and its Applications to Intelligence, CRM and Knowledge Management. Southampton [u.a.] : WTI Press, 2005 (Advances in management information 2). Institutsveröffentlichung: SCAI: Abteilung: Bioinformatik

• Fluck, Juliane; Stitt, Marc; Selbig, Joachim; Hofmann, Martin; Thimm, Oliver: Using named entity recognition for ontology annotation : an experimental approach for Arabidopsis functional genome annotation. In: ECCB'05 Workshop on Biomedical Ontologies and Text Processing : 28 September, 2005 Madrid, Spain. Madrid, 2005 Institutsveröffentlichung: SCAI: Abteilung: BIO

• Gorlach, S. (Hrsg.): CoreGRID Workshop on Integrated Research in Grid Computing : Pisa, IT, 20.-28. November 2005 ; proceedings. Pisa : Università di Pisa, 2005 Institutsveröffentlichung: SCAI Volltext externer Link

• Grigoriev, Dima; Schwarz, Fritz: Generalized Loewy Decomposition of D-Moduels. In: Kauers, Manuel (Hrsg.); Association for Computing Machinery / Special Interest Goup on Symbolic and Algebraic Manipulation: ISSAC 2005 / CD-ROM : proceedings of the 2005 ACM-SIGSAM International Symposium on Symbolic and Algebraic Computation, Beijing, China, July 24-27, 2005. New York, NY : ACM, 2005 Schlagwörter: Partial Differential Equations; D-Modules; Computer-Algebra Institutsveröffentlichung: SCAI: Abteilung: INA
  Abstract: Starting from the well-known factorization of linear ordinary differential equations, we define the generalized Loewy ecomposition for a ${\cal D}$-module. To this end, for any module $I$, overmodules $J\supseteq I$ are constructed. They subsume the conventional factorization as special cases.
  Furthermore, the new concept of the module of relative syzygies $Syz(I,J)$ is introduced. The invariance of this module and its solution space w.r.t. the set of generators is shown. We design an algorithm which constructs the
  Loewy-decomposition for finite-dimensional and some kinds of general ${\cal D}$-modules. These results are applied for solving various second-and third-order linear partial differential equations.

• Grigoriev, Dima; Schwarz, Fritz: Generalized Loewy Decomposition of D-Modules. In: ISSAC 2005 : proceedings of the 2005 ACM-SIGSAM International Symposium on Symbolic and Algebraic Computation, Beijing, China, July 24-27, 2005. New York, NY : ACM Press, 2005, S. 163-170 Schlagwörter: Partial Differential Equations; D-Modules; Computer-Algebra Institutsveröffentlichung: SCAI: Abteilung: INA.CADE
  Abstract: Starting from the well-known factorization of linear ordinary differential
  equations, we define the generalized Loewy decomposition for a
  ${\cal D}$-module. To this end, for any module $I$, overmodules $J\supseteq I$
  are constructed. They subsume the conventional factorization as special
  cases. Furthermore, the new concept of the module of relative syzygies $Syz(I,J)$
  is introduced. The invariance of this module and its solution space w.r.t.
  the set of generators is shown. We design an algorithm which constructs the
  Loewy-decomposition for finite-dimensional and some kinds of general
  ${\cal D}$-modules. These results are applied for solving various second-
  and third-order linear partial differential equations.

• Hanisch, Daniel; Fundel, Katrin; Mevissen, Heinz-Theodor; Zimmer, Ralf; Fluck, Juliane: ProMiner: Rule based protein and gene entity recognition. In: BMC bioinformatics 6 (2005), 1, S. 14 Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Background: Identification of gene and protein names in biomedical text is a challenging task as the corresponding nomenclature has evolved over time. This has led to multiple synonyms for individual genes and proteins, as well as names that may be ambiguous with other gene names or with general English words. The Gene List Task of the BioCreAtIvE challenge evaluation enables comparison of systems addressing the problem of protein and gene name identification on common benchmark data. Methods: The ProMiner system uses a pre-processed synonym dictionary to identify potential name occurrences in the biomedical text and associate protein and gene database identifiers with the detected matches. It follows a rule-based approach and its search algorithm is geared towards recognition of multi-word names [1]. To account for the large number of ambiguous synonyms in the considered organisms, the system has been extended to use specific variants of the detection procedure for highly ambiguous and case-sensitive synonyms. Based on all detected synonyms for one abstract, the most plausible database identifiers are associated with the text. Organism specificity is addressed by a simple procedure based on additionally detected organism names in an abstract. Results: The extended ProMiner system has been applied to the test cases of the BioCreAtIvE competition with highly encouraging results. In blind predictions, the system achieved an F-measure of approximately 0.8 for the organisms mouse and fly and about 0.9 for the organism yeast. http://dx.doi.org/10.1186/1471-2105-6-S1-S14

• Hessler, Gerhard; Zimmermann, Marc; Matter, Hans; Evers, Andreas; Naumann, Thorsten; Lengauer, Thomas; Rarey, Matthias: Multiple-ligand-based virtual screening: Methods and applications of the MTree approach. In: Journal of medicinal chemistry 48 (2005), 21, S. 6575-6584 Institutsveröffentlichung: SCAI
  Abstract: We present a novel approach for ligand-based virtual screening by combining query molecules into a multiple feature tree model called MTree. All molecules are described by the established feature,tree descriptor, which is derived from a topological molecular graph. A new pairwise alignment algorithm leads to a consistent topological molecular alignment based on chemically reasonable matching of corresponding functional groups. These multiple feature tree models find application in ligand-based virtual screening to identify new lead structures for chemical optimization. Retrospective virtual screening with MTree models generated for angiotensin-converting enzyme and the ala receptor on a large candidate database yielded enrichment factors up to 71 for the first 1% of the screened database. MTree models outperformed database searches using single feature trees in terms of hit rates and quality and additionally identified alternative molecular scaffolds not included in any of the query molecules. Furthermore, relevant molecular features, which are known to be important for affinity to the target, are identified by this new methodology. http://dx.doi.org/10.1021/jm050078w

• Iza-Teran, Rodrigo; Lorentz, Rudolph: Lossless compression of meteorological data. In: ERCIM News (2005), 61, S. 41 Institutsveröffentlichung: SCAI Volltext Externer Link

• Jakumeit, Jürgen; Herdy, M.; Nitsche, Michael: Parameter optimization of the sheet metal forming process using an iterative parallel Kriging algorithm. In: Structural and multidisciplinary optimization 29 (2005), 6, S. 498-507 Institutsveröffentlichung: SCAI
  Abstract: Different numerical optimization strategies were used to find an optimized parameter setting for the sheet metal forming process. A parameterization of a time-dependent blank-holder force was used to control the deep-drawing simulation. Besides the already well-established gradient and direct search algorithms and the response surface method the novel Kriging approach was used as an optimization strategy. Results for two analytical and two sheet metal forming test problems reveal that the new Kriging approach leads to a fast and stable convergence of the optimization process. Parallel simulation is perfectly supported by this method. http://dx.doi.org/10.1007/s00158-004-0455-3

• Janoske, Uwe; Dehning, Carsten; Lanfrit, Marco; Habig, Ralph: Boundary data exchange between CFD and radiation. In: Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 6th MpCCI User Forum : February 22nd and 23rd, 2005 at Schloss Birlinghoven, Sankt Augustin ; proceedings. Sankt Augustin : Fraunhofer SCAI, 2005, S. 86-93 Institutsveröffentlichung: SCAI

• Kuhlmann, Annette; Vetter, Ralf-Michael; Lübbing, Christoph; Thole, Clemens-August: Data mining on crash simulation data. In: Perner, Petra (Hrsg.) u.a.: Machine learning and data mining in pattern recognition : 4th international conference, MLDM 2005, Leipzig, Germany, July 9-11, 2005 ; proceedings. Berlin [u.a.] : Springer, 2005, S. 558-569 (Lecture notes in computer science 3587 : Lecture notes in artificial intelligence). Institutsveröffentlichung: SCAI http://dx.doi.org/10.1007/11510888%5F55 Volltext

• Orian-Rousseau, Véronique; Mink, Sigrun; Mengwasser, Jörg; HogenEsch, Harm; Guo, Feng; Thies, Wolf-Gerolf; Hoffmann, Martin; Herrlich, Peter; Ponta, Helmut: Genes upregulated in a metastasizing human colon carcinoma cell line. In: International journal of cancer 113 (2005), 5, S. 699-705 Institutsveröffentlichung: SCAI: Abteilung: BIO http://dx.doi.org/10.1002/ijc.20644

• Revillion, Thomas; Friedrich, Christoph M.; Fluck, Juliane; Hofmann, Martin: Biological and Chemical Entity Recognition from Text Using Conditional Random Fields. In: University Hamburg u.a.: German Conference on Bioinformatics : GCB 2005, Hamburg, October 5th - 7th , 2005. 2005 Institutsveröffentlichung: SCAI

• Rümpler, Christian; Reichert, Frank; Stammberger, Hartwig; Terhoeven, Peter; Berger, Frank: Experimentelle und numerische Untersuchung des Lichtbogenlaufverhaltens. In: Schöpf, Thomas J. (Hrsg.): Kontaktverhalten und Schalten : 18. Fachtagung Albert-Keil-Kontaktseminar vom 5. bis 7. Oktober 2005 an der Universität Karlsruhe. Berlin [u.a.] : VDE-Verlag, 2005, S. 41-48 (VDE-Fachbericht 61). Schlagwörter: Lichtbogen; Niederspannung; Simulation; Experimente; Magnetfeldsonden Institutsveröffentlichung: SCAI: Abteilung: SIAN/
  Abstract: Niederspannungs Leistungsschalter sind in der Lage, Kurzschlussstörme
  selbsttätig zu erkennen und sicher auszuschalten. Beim Öffnen der
  Kontaktstücke in strombegrenzenden Geräten entsteht ein Lichtbogen, der
  eine hohe Gegenspannung erzeugt und damit den Strom deutlich vor Erreichen
  des prospektiven Kurzschlussstroms begrenzt und die Stromflusszeit
  reduziert. Zur Verkürzung der Entwicklungszeit wird angestrebt, das
  Verhalten dieses Lichtbogens vorherzusagen. Dazu werden in diesem Beitrag
  erste Ergebnisse experimenteller Untersuchungen und numerischer
  Berechnungen an parallelen Laufschienenanordnungen vorgestellt. Zur
  Beobachtung des Lichtbogenlaufverhaltens werden bei den Experimenten
  zusätzlich zu optischer Beobachtung Magnetfeldsonden eingesetzt, um den
  Schwerpunkt des Stromflusses zu detektieren. Bei der Simulation wird für
  die Lösung des Magnetfelds und der Strömung jeweils ein separates Programm
  eingesetzt, deren Ergebnisse kontinuierlich ausgetauscht werden. Erste
  Ergebnisse zeigen eine gute Übereinstimmung der berechneten Bogenspannung
  und des anfänglichen Bogenlaufverhaltens mit gemessenen Werten.

• Scholl, Uwe: New mapping schemes and tools. In: Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 6th MpCCI User Forum : February 22nd and 23rd, 2005 at Schloss Birlinghoven, Sankt Augustin ; proceedings. Sankt Augustin : Fraunhofer SCAI, 2005, S. 106-111 Institutsveröffentlichung: SCAI

• Thole, Clemens-August: Datenkompression von Simulationsergebnissen : Data compression method for irregular grid data e.g. automobile crash simulation data, using adjacent grid position proximity information for providing approximated parameter value. In: Europäisches Patentblatt (2005), 20050316 Institutsveröffentlichung: SCAI
  Abstract: Die Erkenntnis der vorliegenden Erfindung besteht darin, dass auch Daten, die fuer einen Parameter fuer jede Gitterposition von Gitterpositionen eines unregelmaessigen Gitters einen Parameterwert sowie einen gemeinsamen Bestimmungsblock aufweisen, der Nachbarschaftsinformationen umfasst, die fuer jede Gitterposition angeben, zu welcher oder welchen der Gitterpositionen die jeweilige Gitterposition benachbart ist, mit hoher Komprimierungsrate komprimiert werden koennen, wenn ihre Nachbarschaftsinformationen verwendet werden, um fuer den Parameterwert einer vorbestimmten Gitterposition einen Approximationswert aus dem Parameterwert zumindest einer anderen Gitterposition zu ermitteln, der zu der vorbestimmten Gitterposition benachbart ist. Eine Abbildung eines approximierten Parameterwertes auf einen interpolierten Wert, aus dem in Verbindung mit dem Approximationswert auf denselben rueckgeschlossen werden kann, wie z. B. die Differenz zu dem Approximationswert, und auf eine Angabe, aus der sich der Approximationswert ermitteln laesst, ergibt bei entsprechender Anwendung dieser Vorgehensweise fuer mehrere Gitterpositionen kleine interpolierte Werte, die zur Bitdarstellung bzw. Codierung wiederum nur weniger Bits als die urspruengliche Darstellung der Parameterwerte benoetigen, sowie lediglich eine im Wesentlichen nur unverkuerzt darstellbare Angabe, aus der der Approximationswert ermittelbar ist.
  Abstract: WO2005006561 A UPAB: 20050311 NOVELTY - The method has the data representing the parameter values for each grid position (56) of an irregular grid (58) compressed by using proximity information for the adjacent grid positions to a given grid position within the same grid group (60,62,64,66), for approximating the parameter value for at least one adjacent grid position, with mapping of the approximated parameter value onto an interpolated value. DETAILED DESCRIPTION - Also included are INDEPENDENT CLAIMS for the following: (A) a data compression device for irregular grid data; (B) a data decompression method for irregular grid data; (C) a data decompression device; (D) a computer program for data compression or decompression USE - The data compression method is used for parameter data for each grid position of an irregular grid, e.g. for automobile crash simulation data. ADVANTAGE - Method allows small interpolated values with fewer bits than original parameter values. DESCRIPTION OF DRAWING(S) - The figure shows a schematic representation of part of an irregular grid with division of the grid positions into groups. Grid positions 56 Irregular grid 58 Grid position groups 60,62,64,66 Dwg.5/14

• Trochim, Sabine; Dach, Holger: Extracting Pathways from Huge Literature Networks : Poster. Hamburg, 2005 Institutsveröffentlichung: SCAI: Abteilung: Bioinformatik

• Vet, Paul van der; Huibers, Theo; Binz, Pierre-Alain; Hofmann, Martin: ESF workshop on 'sustainability and governance of web and GRID resources in functional genomics'. In: Comparative and functional genomics 6 (2005), 5-6, S. 307-310 Institutsveröffentlichung: SCAI: Abteilung: Bioinformatik http://dx.doi.org/10.1002/cfg.488

• Wäldrich, Oliver; Ziegler, Wolfgang; CoreGrid - European Research Network on Foundations, Software Infrastructures and Applications for Large Scale Distributed, GRID and Peer-to-Peer Technologies; Institute on Resource Management and Scheduling: A Meta-Scheduling Service for Co-allocating Arbitrary Types of Resources. 2005 (CoreGrid technical report; TR-0010) Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

• Wang, Y.; Bui Thi, L.T.; Friedrich, Christoph M.; Zimmermann, M.; Algorri, M.; Noltemeier, Hartmut; Hofmann, Martin: CSR - Chemical Structure Recognition from Images. In: University Hamburg u.a.: German Conference on Bioinformatics : GCB 2005, Hamburg, October 5th - 7th , 2005. 2005 Institutsveröffentlichung: SCAI

• Wermter, Joachim; Fluck, Juliane; Stroetgen, Jannik; Geißler, Stefan; Hahn, Udo: Recognizing noun phrases in biomedical text : an evaluation of lab prototypes and commercial chunkers. In: Hahn, Udo (Hrsg.) u.a.: SMBM 2005 : first International Symposium on Semantic Mining in Biomedicine (SMBM), EBI, Hinxton, UK, 10-12 April 2005. Aachen : RWTH, 2005, 9 S. (CEUR workshop proceedings 148). Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext Externer Link

• Wieder, Philipp; Ziegler, Wolfgang; CoreGrid - European Research Network on Foundations, Software Infrastructures and Applications for Large Scale Distributed, GRID and Peer-to-Peer Technologies; Institute on Resource Management and Scheduling: Bringing Knowledge to Middleware - Grid Scheduling Ontology. 2005 (CoreGrid technical report; TR-0008) Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: The Grid paradigm implies the sharing of a variety of resources across multiple administrative domains. Assuming that such an environment is highly dynamic, it is essential to abstract potential drawbacks away from resource users and resource providers. One crucial aspect in designing and operating Grids to gain the respective abstraction is the provision of a sophisticated scheduling and resource management framework. Experience shows that scheduling a single resource like an HPC system is already a challenge, but the co-ordinated scheduling of multiple resources to automatically process a complex work flow is impossible if the capabilities of resources are not a priori known. We propose to make scheduling-specific parts of such knowledge exploitable by introducing a scheduling domain ontology. This ontology provides a common semantic understanding to be shared between the components involved in the scheduling process. By agreeing upon and integrating such an ontology we increase the automation level and make usage and administration of Grids easier. Volltext

• Wolf, Klaus: Multi-physics simulation through code coupling. In: Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 6th MpCCI User Forum : February 22nd and 23rd, 2005 at Schloss Birlinghoven, Sankt Augustin ; proceedings. Sankt Augustin : Fraunhofer SCAI, 2005, S. 12-19 Institutsveröffentlichung: SCAI

• Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 6th MpCCI User Forum : February 22nd and 23rd, 2005 at Schloss Birlinghoven, Sankt Augustin ; proceedings. Sankt Augustin : Fraunhofer SCAI, 2005 Institutsveröffentlichung: SCAI

• Zacharias, Albert; Rümpler, Christian: Electric arc simulations. In: Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 6th MpCCI User Forum : February 22nd and 23rd, 2005 at Schloss Birlinghoven, Sankt Augustin ; proceedings. Sankt Augustin : Fraunhofer SCAI, 2005, S. 122-125 Institutsveröffentlichung: SCAI

• Zimmermann, Marc; Le Thuy, Buy Thi; Hofmann, Martin: Combating illiteracy in chemistry: towards computer-based chemical structure reconstruction. In: ERCIM News (2005), 60, S. 40-41 Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext externer Link

• Zimmermann, Marc; Fluck, Juliane; Bui Thi, Le Thuy; Kolárik, Corinna; Kumpf, Kai; Hofmann, Martin: Information extraction in the life sciences : perspectives for medicinal chemistry, pharmacology and toxicology. In: Current topics in medicinal chemistry 5 (2005), 8, S. 785-796 Schlagwörter: information extraction; named entity recognition; chemical structure reconstruction; biological effects; semantic mediation Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Information extraction approaches have been successfully applied to mine the scientific literature in biology and medicine. So far, the main focus of research and development in this domain was on the recognition and extraction of gene and protein names in the context of molecular biology and genome research and on disease names and other medical terms in the context of clinical research. Similar to biology and medical sciences, medicinal chemistry, pharmacology and toxicology are descriptive sciences. However, information extraction approaches in these disciplines encounter a number of problems that are specific to the fact that these scientific areas are essentially centred at chemical compounds and their structures. In this review, we will give a short overview on general information extraction strategies in the life sciences and we will introduce new approaches to apply information extraction to the domain of pharmacology, medicinal chemistry and toxicology. Finally, we will emphasize on how information extraction approaches will support public and commercial research in medicinal chemistry, pharmacology and toxicology by linking information on chemical structures to biological information.

• Zimmermann, Martin; Friedrich, Christoph M.; Algorri, M.E.: Combating illiteracy in chemistry: towards computer-based chemical structure reconstruction : 1st German Conference on Chemoinformatics, 2005, Goslar. 2005 Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext

2004

• Baeuerle, Christof; Thole, Clemens-August; Trottenberg, Ulrich: DesParO - A Design Parameter Optimisation Toolbox using an Iterative Kriging Algorithm. In: ERCIM News (2004), 56, S. 32-33 Institutsveröffentlichung: SCAI: Abteilung: NUSO Volltext externer Link

• Benkner, Siegfried; Brandes, Thomas: Compiling data-parallel programs for clusters of SMPs. In: Concurrency and computation 16 (2004), 2-3, S. 111-132 Institutsveröffentlichung: SCAI
  Abstract: Clusters of shared-memory multiprocessors (SMPs) have become the most promising parallel computing platforms for scientific computing. However, SMP clusters significantly increase the complexity of user application development when using the low-level application programming interfaces MPI and OpenMP, forcing users to deal with both distributed-memory and shared-memory parallelization details. In this paper we present extensions of High Performance Fortran (HPF) for SMP clusters which enable the compiler to adopt a hybrid parallelization strategy, efficiently combining distributed-memory with shared-memory parallelism. By means of a small set of new language features, the hierarchical structure of SMP clusters may be specified. This information is utilized by the compiler to derive inter-node data mappings for controlling distributed-memory parallelization across the nodes of a cluster and intra-node data mappings for extracting shared-memory parallelism within nodes. Additional mechanisms are proposed for specifying inter- and intra-node data mappings explicitly, for controlling specific shared-memory parallelization issues and for integrating OpenMP routines in HPF applications. The proposed features have been realized within the ADAPTOR and VFC compilers. The parallelization strategy for clusters of SMPs adopted by these compilers is discussed as well as a hybrid-parallel execution model based on a combination of MPI and OpenMP. Experimental results indicate the effectiveness of the proposed features. http://dx.doi.org/10.1002/cpe.767

• Bilowsky, H.; Ziegler, R.; Hofmann, Martin; Breton, Vincent; Jones, C..: Grid enabled pharmaceutical R&D : PharmaGrids. In: HealthGrid: White paper / HealthGrid. Pont du Chateau : HealthGrid Association, 2004, S. 33-36 Institutsveröffentlichung: SCAI: Abteilung: BIO

• Crass, T.; Antes, I.; Basekow, W.; Bork, P.; Buning, C.; Christensen, M.; Claussen, H.; Ebeling, C.; Ernst, P.; Gailus-Durner, V.; Glatting, K.H.; Gohla, R.; Gössling, F.; Grote, K.; Heidtke, K.; Herrmann, A.; O'Keeffe, S.; Kiesslich, O.; Kolibal, S.; Korbel, J.O.; Lengauer, Thomas; Liebich, I.; Linden, M. van der; Luz, H.; Meissner, K.; Mering, C. van; Mevissen, H.T.; Mewes, H.W.; Michael, H.; Mokrejs, M.; Müller, T.; Pospisil, H.; Rarey, M.; Reich, J.G.; Schneider, R.; Schomburg, D.; Schulze-Kremer, S.; Schwarzer, K.; Sommer, I.; Springstubbe, Stephan; Suhai, S.; Thoppae, G.; Vingron, M.; Warfsmann, J.; Werner, T.; Wetzler, V.; Wingender, E.; Zimmer, R.: The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. In: Bioinformatics 20 (2004), 2, S. 268-270 Institutsveröffentlichung: SCAi
  Abstract: The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single web portal. The 'Guided Solution Finder' which is available through the HNB portal helps users to locate the appropriate resources to answer their queries by employing a detailed, tree-like questionnaire. Furthermore, automated complex tool cascades ('tasks'), involving resources located on different servers, have been implemented, allowing users to perform comprehensive data analyses without the requirement of further manual intervention for data transfer and re-formatting. Currently, automated cascades for the analysis of regulatory DNA segments as well as for the prediction of protein functional properties are provided. http://dx.doi.org/10.1093/bioinformatics/btg398

• Der, Uwe; Ernst, Thilo; Eckert, Klaus-Peter; Falkner, Jürgen; Hoheisel, Andreas; Pfreundt, Franz-Joseph; Weisbecker, Anette; Ziegler, Wolfgang: Fraunhofer grid alliance - From grid-based e-science to industrial applications. In: ERCIM News (2004), 59, S. 20-21 Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext externer Link

• Fricker, Patrick C.; Gastreich, Marcus; Rarey, Matthias: Automated drawing of structural molecular formulas under constraints. In: Journal of chemical information and computer sciences 44 (2004), 3, S. 1065-1078 Institutsveröffentlichung: SCAI
  Abstract: In this paper, we present a new algorithm for automated drawing of 2D structural formulas of molecules. The algorithm is based on the classical scheme of a drawing queue placing the molecular fragments in a sequential way. We extend the concept of so-called prefabricated units developed for complex ring systems to automatically created drawing units for chains and rings which will then be assembled in a sequential fashion. The approach is fast and can be naturally extended to the problem of drawing molecules with common core structures. Further on, we present an algorithm that allows the drawing of 2D structural formulas under directional constraints assigned to a subset of bonds. Since no numerical optimization is necessary, the algorithm creates drawings of small organic molecules on the order of 500 structures per second. The new algorithm is relevant for all kinds of prediction and analysis software presenting a large number of probably similar molecular structures to the user of the software. http://dx.doi.org/10.1021/ci049958u

• Garms, Onno; Heckmann, Ralf; Rank, Stefan: Contpack - Maximising the Volume Utilisation of Containers. In: ERCIM News (2004), 56, S. 18-20 Institutsveröffentlichung: SCAI: Abteilung: OPT Volltext externer Link

• Gaspar, F. J.; Lisbona, F. J.; Oosterlee, Cornelis W.; Wienands, Roman: Systematic comparison of coupled and distributive smoothing in multigrid for the poroelasticity system. In: Numerical linear algebra with applications 11 (2004), 2-3, S. 93-113 Institutsveröffentlichung: SCAI http://dx.doi.org/10.1002/nla.372

• Gieger, Christian; Hanisch, Daniel; Fluck, Juliane; Mevissen, Heinz-Theodor; Tresch, Achim; Deneke, Hartwig: Using Text Mining Networks for the Context Specific Interpretation of Gene Expression Data. In: Biometrical journal 46 (2004), S1, S. 56 Institutsveröffentlichung: SCAI: Abteilung: BIO http://dx.doi.org/10.1002/bimj.200490260

• Grigoriev, D.; Schwarz, Fritz: Factoring and Solving Linear Partial Differential Equations. In: Computing 73 (2004), 2, S. 179-197 Institutsveröffentlichung: SCAI
  Abstract: The problem of factoring a linear partial differential operator is studied. An algorithm is designed which allows one to factor an operator when its symbol is separable, and if in addition the operator has enough right factors then it is completely reducible. Since finding the space of solutions of a completely reducible operator reduces to the same for its right factors, we apply this approach and execute a complete analysis of factoring and solving a second-order operator in two independent variables. Some results on factoring third-order operators are exhibited. http://dx.doi.org/10.1007/s00607-004-0073-3

• Grund, Helmut; Ziegler, Wolfgang: Resource management in an optical grid testbed. In: ERCIM News (2004), 59, S. 37-38 Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext externer Link

• Häfner, Frieder; Stüben, Klaus: Simulation and parameter identification of Oswald's salt-pool experiments with the SAMG multigrid-solver in the transport code MODCALIF. In: Kovar, K.: FEM Modflow : International Conference on Finite Element Models, MODFLOW, and More: Solving Groundwater Problems : 13 - 16 September 2004, Karlovy Vary, Czech Republic. Prague, 2004 Institutsveröffentlichung: SCAI

• Hanisch, Daniel; Fundel, Katrin; Mevissen, Heinz-Theodor; Zimmer, Ralf; Fluck, Juliane: ProMiner: Organism specific protein name detection using approximate string matching. In: European Molecular Biology Organization: A critical assessment of text mining methods in molecular biology : EMBO Workshop, Granada, Spain, March 28-31, 2004. Heidelberg : EMBO, 2004 Institutsveröffentlichung: SCAI: Abteilung: BIO

• Hanisch, Daniel; Sohler, Florian; Zimmer, Ralf: TOPNET: an application for interactive analysis of expression data and biological networks. In: Bioinformatics 20 (2004), 9, S. 1470-1471 Institutsveröffentlichung: SCAI
  Abstract: ToPNet is a new tool for the combined visualization and exploration of gene networks and expression data. ToPNet provides various ways of restricting, manipulating and combining biological networks according to annotation data (e.g. Gene Ontology terms) and presents results to the user via different visualization procedures and hyperlinks to the underlying data sources. To easily identify relevant parts of the network, ToPNet provides a method of detecting significant subnetworks with respect to expression measurements. As ToPNet is a pure JAVA application with additional scripting capabilities, it is well-suited as a test-bed for algorithm development and exploratory biological data analysis alike. http://dx.doi.org/10.1093/bioinformatics/bth096

• Hofmann, Martin; Solomonides, T.; Maglaveras, N.: GRIDs for epidemiological studies. In: HealthGrid: White paper / HealthGrid. Pont du Chateau : HealthGrid Association, 2004, S. 37-44 Institutsveröffentlichung: SCAI: Abteilung: BIO

• Krapp, Michael (Red.); Bolduan, Gordon (Red.): Jahresbericht 2002/2003 / Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI. Sankt Augustin : Fraunhofer SCAI, 2004 (Jahresbericht / Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI) Institutsveröffentlichung: SCAI Volltext

• Kumpf, Kai; Hofmann, Martin: Bioinformatics in the semantic grid. In: ERCIM News (2004), 59, S. 54-55 Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext externer Link

• Lengauer, Thomas; Lemmen, Christian; Rarey, Matthias; Zimmermann, Marc: Novel technologies for virtual screening. In: Drug discovery today 9 (2004), 1, S. 27-34 Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: There are several methods for virtual screening of databases of small organic compounds to find tight binders to a given protein target. Recent reviews in Drug Discovery Today have concentrated on screening by docking and by pharmacophore searching. Here, we complement these reviews by focusing on virtual screening methods that are based on analyzing ligand similarity on a structural level. Specifically, we concentrate on methods that exploit structural properties of the complete ligand molecules, as opposed to using just partial structural templates, such as pharmacophores. The in silica procedure of virtual screening (VS) and its relationship to the experimental procedure, HTS, is discussed, new developments in the field are summarized and perspectives on future research are offered. http://dx.doi.org/10.1016/S1359-6446(04)02939-3

• Öhsen, Niklas von; Sommer, Ingolf; Lengauer, Thomas: ARBY - automatic protein-structure prediction using profile- profile alignment and confidence measures. In: Bioinformatics 20 (2004), 14, S. 2228-2235 Institutsveröffentlichung: SCAI
  Abstract: Motivation: Arby is a new server for protein structure prediction that combines several homology-based methods for predicting the three-dimensional structure of a protein, given its sequence. The methods used include a threading approach, which makes use of structural information, and a profile-profile alignment approach that incorporates secondary structure predictions. The combination of the different methods with the help of empirically derived confidence measures affords reliable template selection. Results: According to the recent CAFASP3 experiment, the server is one of the most sensitive methods for predicting the structure of single domain proteins. The quality of template selection is assessed using a fold-recognition experiment. http://dx.doi.org/10.1093/bioinformatics/bth232

• Sohler, Florian; Hanisch, Daniel; Zimmer, Ralf: New methods for joint analysis of biological networks and expression data. In: Bioinformatics 20 (2004), 10, S. 1517-1521 Institutsveröffentlichung: SCAI
  Abstract: Biological networks, such as protein interaction, regulatory or metabolic networks, derived from public databases, biological experiments or text mining can be useful for the analysis of high-throughput experimental data. We present two algorithms embedded in the ToPNet application that show promising performance in analyzing expression data in the context of such networks. First, the Significant Area Search algorithm detects subnetworks consisting of significantly regulated genes. These subnetworks often provide hints on which biological processes are affected in the measured conditions. Second, Pathway Queries allow detection of networks including molecules that are not necessarily significantly regulated, such as transcription factors or signaling proteins. Moreover, using these queries, the user can formulate biological hypotheses and check their validity with respect to experimental data. All resulting networks and pathways can be explored further using the interactive analysis tools provided by ToPNet program. http://dx.doi.org/10.1093/bioinformatics/bth112

• Springstubbe, Stephan; Klein, Juergen; Krämer-Fuhrmann, Ottmar: Numerical Simulation through Web Services. In: ERCIM News (2004), 56, S. 51-53 Institutsveröffentlichung: SCAI: Abteilung: WEB Volltext externer Link

• Zimmermann, Marc; Tresch, A.; Maass, A.; Hofmann, M.: Drilling into a HTS data set of e.coli : Poster. 2004 Institutsveröffentlichung: SCAI: Abteilung: BIO

2003

• Ahrem, Regin; Beckert, Armin; Neumann, Jens; Wendland, Holger: Scattered data interpolation library. In: Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 4th MpCCI User Forum : March 12th & 13th, 2003, Schloss Birlinghofen, Sankt augustin, Germany ; book of abstracts. Sankt Augustin : Fraunhofer SCAI, 2003, S. 15 Institutsveröffentlichung: SCAI

• Albrecht, Mario; Hoffmann, Daniel; Evert, Bernd O.; Schmitt, Ina; Wüllner, Ullrich; Lengauer, Thomas: Structural modeling of ataxin-3 reveals distant homology to adaptins. In: Proteins 50 (2003), 2, S. 355-370 Institutsveröffentlichung: SCAI
  Abstract: Spinocerebellar ataxia type 3 (SCA3) is a polyglutamine disorder caused by a CAG repeat expansion in the coding region of a gene encoding ataxin-3, a protein of yet unknown function. Based on a comprehensive computational analysis, we propose a structural model and structure-based functions for ataxin-3. Our predictive strategy comprises the compilation of multiple sequence and structure alignments of carefully selected proteins related to ataxin-3. These alignments are consistent with additional information on sequence motifs, secondary structure, and domain architectures. The application of complementary methods revealed the homology of ataxin-3 to ENTH and VHS domain proteins involved in membrane trafficking and regulatory adaptor functions. We modeled the structure of ataxin-3 using the adaptin AP180 as a template and assessed the reliability of the model by comparison with known sequence and structural features. We could further infer potential functions of ataxin-3 in agreement with known experimental data. Our database searches also identified an as yet uncharacterized family of proteins, which we named josephins because of their pronounced homology to the Josephin domain of ataxin-3. http://dx.doi.org/10.1002/prot.10280

• Baeuerle, Christof: Process parameter optimisation. In: Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 4th MpCCI User Forum : March 12th & 13th, 2003, Schloss Birlinghofen, Sankt augustin, Germany ; book of abstracts. Sankt Augustin : Fraunhofer SCAI, 2003, S. 28 Institutsveröffentlichung: SCAI

• Becker, A.; Chen, J.; Zien, Alexander; Sochivko, D.; Normann, S.; Schramm, J.; Elger, C.E.; Wiestler, O.D.; Blumcke, I.: Stage and subfield associated hippocampal gene expression patterns in experimental and human temporal lobe epilepsy. In: Journal of neuropathology and experimental neurology 62 (2003), S. 104 Institutsveröffentlichung: SCAI

• Clees, Tanja; Stüben, Klaus: Algebraic multigrid for industrial semiconductor device simulation. In: Bänsch, Eberhard (Hrsg.): Challenges in Scientific Computing - CISC 2002 : proceedings of the Conference "Challenges in Scientific Computing", Berlin, October 2-5, 2002. 2003, S. 110-130 (Lecture notes in computational science and engineering 35). Institutsveröffentlichung: SCAI

• Dehning, Carsten: MpCCI-adapters to commercial CFD/FEM applications using the code API's. In: Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 4th MpCCI User Forum : March 12th & 13th, 2003, Schloss Birlinghofen, Sankt augustin, Germany ; book of abstracts. Sankt Augustin : Fraunhofer SCAI, 2003, S. 12 Institutsveröffentlichung: SCAI

• Dehning, Carsten: Multidisciplinary engineering at SCAI. In: Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 4th MpCCI User Forum : March 12th & 13th, 2003, Schloss Birlinghofen, Sankt augustin, Germany ; book of abstracts. Sankt Augustin : Fraunhofer SCAI, 2003, S. 14 Institutsveröffentlichung: SCAI

• Finger, F.; Schörle, C.; Zien, Alexander; Gebhard, P.; Goldring, M.B.; Aigner, T.: Molecular phenotyping of human chondrocyte cell-lines T/C-28a2, T/C-28a4, and C-28/I2. In: Arthritis & rheumatism 48 (2003), 12, S. 3395-3403 Institutsveröffentlichung: SCAI
  Abstract: Objective. Because the immortalized chondrocyte cell lines C-28/I2, T/C-28a2, and T/C-28a4 have become a common tool in cartilage research, permitting investigations in a largely unlimited and standardized manner, we investigated the molecular phenotype of these cell lines by gene expression profiling. Methods. Complementary DNA-array analysis as well as online quantitative polymerase chain reaction were used to identify the gene expression profiles of the 3 cell lines cultured in monolayer and alginate beads, as compared with the expression profiles of cultured human adult primary chondrocytes. Results. A similar, but not identical, gene expression profile was established for all 3 cell lines. SOX9 was expressed at a significant level in all 3 cell lines. Extracellular matrix proteins and matrix-degrading proteases were rarely expressed. In contrast, genes involved in the cell cycle were strongly up-regulated, as compared with the expression levels in physiologic chondrocytes. Conclusion. The expression of SOX9, the master gene of chondrocytic cell differentiation, reflects the basically chondrocytic phenotype of these cells. However, the major issue appears to be that these cell lines mainly proliferate and show less expression of genes involved in matrix synthesis and turnover. In this respect, C-28/I2 cells display the highest levels of matrix-anabolic and matrix-catabolic genes and thus are presumably preferable for use in investigating chondrocyte anabolic and catabolic activity and its regulation. None of the 3 cell lines appears to be a direct substitute for primary chondrocytes. A successful approach will have to validate the findings obtained with chondrocyte cell lines by using primary chondrocytes or cartilage-tissue cultures. This would permit the establishment of reproducible in vitro models and subsequently allow investigators to relate the findings to the physiologic situation. http://dx.doi.org/10.1002/art.11341

• Galbas, Hans-Georg; Kolp, Otto: Multiphase overpartitioning in crashworthiness simulation. In: Onate, E. (Hrsg.) u.a.: VII International Conference on Computational Plasticity COMPLAS 2003. Barcelona : CIMNE, 2003 Institutsveröffentlichung: SCAI: Abteilung: NUSO

• Gastreich, Marcus; Gale, Julian D.; Marian, Christel M.: Charged-particle potential for boron nitrides, silicon nitrides, and borosilazane ceramics : Derivation of parameters and probing of capabilities. In: Physical review / B, Condensed matter and materials physics 68 (2003), 9, Art. 094110, 17 S. Institutsveröffentlichung: SCAI
  Abstract: A classical pair potential, augmented by three-body interactions, for the modeling of borosilazane ceramics has been derived on the basis of both experimental and ab initio data. The primary goals were a good description of structural parameters and applicability in molecular dynamics. Furthermore, major challenges were to enable bond breaking and to avoid Coulomb collapse during simulations. This has been achieved by long-range, exponentially damped, analytical forms and the inclusion of short-range Coulomb tapering functions. We report on the fitting procedure, discuss the analytical forms employed, and demonstrate the abilities of the potential by comparing to ab initio calculations and experiments. http://dx.doi.org/10.1103/PhysRevB.68.094110

• Gieger, Christian; Deneke, Hartwig; Fluck, Juliane: The Future of Text Mining in Genome-based Clinical Research. In: Biosilico 3 (2003), 1, S. 97-102 Institutsveröffentlichung: SCAI: Abteilung: BIO http://dx.doi.org/10.1016/S1478-5382(03)02336-9

• Gieger, Christian; Kschischo, Maik; Kern, Rainer; Steinhauser, Martin; Tolle, Ralf: Improving SNP genotyping results by introducing Gaussian mixture models for genotype calling. In: Spang, Rainer (Hrsg.) u.a.; Max-Planck-Institute for Molecular Genetics Berlin u.a.: Currents in computational molecular biology 2003 : RECOMB 2003, Berlin ; extended poster abstracts from the poster sessions. Berlin, 2003, S. 9-10 Schlagwörter: SNP; clustering; Gaussian mixture model; genotyping; quality control Institutsveröffentlichung: SCAI

• Gurskii, V.V.; Samsonov, A. M.; Schwarz, Fritz: Classical and nonclassical symmetries of the nonlinear equation with dispersion and dissipation. In: Technical physics 48 (2003), 11, S. 1359-1363 Institutsveröffentlichung: SCAI http://dx.doi.org/10.1134/1.1626765

• Hanisch, Daniel; Fluck, Juliane; Mevissen, Heinz; Zimmer, Ralf: Playing biology's name game: identifying protein names in scientific texts. In: Altman, R.B. (Hrsg.) u.a.: Pacific Symposium on Biocomputing 2003 : Kauai, Hawaii, 3 - 7 January 2003. Singapore : World Scientific Publishing, 2003, S. 403-414 Institutsveröffentlichung: SCAI: Abteilung: BIO

• Hanisch, Daniel; Sohler, Florian; Zimmer, Ralf: ToPNet - an application for interactive analysis of expression data and biological networks. In: Spang, Rainer (Hrsg.) u.a.; Max-Planck-Institute for Molecular Genetics Berlin u.a.: Currents in computational molecular biology 2003 : RECOMB 2003, Berlin ; extended poster abstracts from the poster sessions. Berlin, 2003, S. 301-302 Schlagwörter: expression data; biological networks; ToPNet Institutsveröffentlichung: SCAI

• Hofmann, Detlef W.M.; Apostolakis, Joannis: Crystal structure prediction by data mining. In: Journal of molecular structure 647 (2003), 1-3, S. 17-39 Institutsveröffentlichung: SCAI http://dx.doi.org/10.1016/S0022-2860(02)00519-7

• Joppich, Wolfgang; Quaas, Johannes: Coupling General Circulation Models on a Meta-computer. In: Computational science - ICCS 2003. Berlin [u.a.] : Springer, 2003, S. 161-170 (Lecture notes in computer science 2658). Institutsveröffentlichung: SCAI: Abteilung: SIAN http://dx.doi.org/10.1007/3-540-44862-4%5F18 Volltext

• Karabek, Ute: MpCCI 2.0 coupling regions and interpolation types. In: Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 4th MpCCI User Forum : March 12th & 13th, 2003, Schloss Birlinghofen, Sankt augustin, Germany ; book of abstracts. Sankt Augustin : Fraunhofer SCAI, 2003, S. 5 Institutsveröffentlichung: SCAI

• Knorr, T.; Obermayr, F.; Bartnik, E.; Zien, Alexander; Aigner, Thomas: YKL-39 (chitinase 3-like protein 2), but not YKL-40 (chitinase 3-like protein 1), is up regulated in osteoarthritic chondrocytes. In: Annals of the rheumatic diseases 62 (2003), 10, S. 995-998 Institutsveröffentlichung: SCAI
  Abstract: Objective: To investigate quantitatively the mRNA expression levels of YKL-40, an established marker of rheumatoid and osteoarthritic cartilage degeneration in synovial fluid and serum, and a closely related molecule YKL-39, in articular chondrocytes. Methods: cDNA array and online quantitative polymerase chain reaction (PCR) were used to measure mRNA expression levels of YKL-39 and YKL-40 in chondrocytes in normal, early degenerative, and late stage osteoarthritic cartilage samples. Results: Expression analysis showed high levels of both proteins in normal articular chondrocytes, with lower levels of YKL-39 than YKL-40. Whereas YKL-40 was significantly down regulated in late stage osteoarthritic chondrocytes, YKL-39 was significantly up regulated. In vitro both YKLs were down regulated by interleukin 1beta. Conclusions: The up regulation of YKL-39 in osteoarthritic cartilage suggests that YKL-39 may be a more accurate marker of chondrocyte activation than YKL-40, although it has yet to be established as a suitable marker in synovial fluid and serum. The decreased expression of YKL-40 by osteoarthritic chondrocytes is surprising as increased levels have been reported in rheumatoid and osteoarthritic synovial fluid, where it may derive from activated synovial cells or osteophytic tissue or by increased matrix destruction in the osteoarthritic joint. YKL-39 and YKL-40 are potentially interesting marker molecules for arthritic joint disease because they are abundantly expressed by both normal and osteoarthritic chondrocytes. http://dx.doi.org/10.1136/ard.62.10.995

• Kuhlmann, A.; Thole, Clemens-August; Trottenberg, Ulrich: AUTOBENCH/AUTO-OPT : towards an integrated construction environment for virtual prototyping in the automotive industry. In: Dongarra, Jack (Hrsg.) u.a.: Recent advances in parallel virtual machine and message passing interface : 10th European PVM/MPI User's Group Meeting, Venice, Italy, September 29-October 2, 2003 ; proceedings. Berlin [u.a.] : Springer, 2003, S. 686-690 (Lecture notes in computer science 2840). Institutsveröffentlichung: SCAI: Abteilung: NUSO.AUTOBENCH
  Abstract: The present paper describes two cooperative projects (AUTO-BENCH and AUTO-OPT) carried out with partners in the automotive industries (AUDI, BMW, DaimlerChrysler, Karmann and Porsche), software vendors of simulation software (ESI, INTES, INPRO, SFE) and technology providers (Uni Stuttgart, FhG-SCAI and DLR-SISTEC). Both projects aim at the development of integrated working environments for virtual automotive prototypes. Special focus is on simulation of functional behaviour of the car body, production of its parts and their improvement. New technologies have been developed for the handling of numerical grids, integration of CAE tools, numerical algorithms and visualisation. Parallel computing is supported throughout the projects on a simulation level as well as for optimisation purposes. Ongoing work concentrates on the interactive simulation and optimisation as well as the reuse of the vast amount of resulting data. Volltext

• Leventi-Peetz, A.-M.; Kharalashvili, Maka: Construction of curves and surfaces from scattered data. In: Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 4th MpCCI User Forum : March 12th & 13th, 2003, Schloss Birlinghofen, Sankt augustin, Germany ; book of abstracts. Sankt Augustin : Fraunhofer SCAI, 2003, S. 24-25 Institutsveröffentlichung: SCAI

• Leventi-Peetz, A.-M.; Kharalashvili, Maka: Design and manufacturing using D-NURBS Tool. In: Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 4th MpCCI User Forum : March 12th & 13th, 2003, Schloss Birlinghofen, Sankt augustin, Germany ; book of abstracts. Sankt Augustin : Fraunhofer SCAI, 2003, S. 26 Institutsveröffentlichung: SCAI

• Li, Ziming; Schwarz, Fritz; Tsarev, Serguei: Factoring systems of linear PDEs with finite-dimensional solution space. In: Journal of symbolic computation 36 (2003), 3-4, S. 443-471 Institutsveröffentlichung: SCAI: Abteilung: INA
  Abstract: A D-finite system is a finite set of linear homogeneous partial differential equations in several independent and dependent variables, whose solution space is of finite dimension. Let L be a D-finite system with rational function coefficients. We present an algorithm for computing all hyperexponential solutions of L, and an algorithm for computing all D-finite systems whose coefficients are also rational functions, and whose solutions are contained in the solution space of L. http://dx.doi.org/10.1016/S0747-7171(03)00090-7

• Lorentz, R.A.; Narcowich, F.J.; Ward, J.D.: Collocation discretizations of the transport equation with radial basis functions. In: Applied mathematics and computation 145 (2003), 1, S. 97-116 Institutsveröffentlichung: SCAI
  Abstract: In this paper, a new gridless method for numerically solving hyperbolic partial differential equations is presented. This method uses collocation based on Hermite interpolation at scattered sites at each time step. The basis can be chosen at each time step, which makes the approach adaptive and allows flexibility. The goal of this paper is to demonstrate the potential of this adaptive, flexible model which includes the ability to use scattered sites in a multi-dimensional setting with compactly supported radial functions. To illustrate the method and to compare it with known results, we analyze a certain transport problem in detail. When combined with an implicit time discretization and applied to smooth solutions, we show that the method yields spectral rates of convergence in the spatial domain. The implicit time discretization makes possible time steps of a size appropriate to the smoothness of the solution. http://dx.doi.org/10.1016/S0096-3003(02)00472-1

• Maaß, Astrid; Scholz, J.; Moser, A.: Modeled ligand-protein complexes elucidate the origin of substrate specificity and provide insight into catalytic mechanisms of phenylalanine hydroxylase and tyrosine hydroxylase. In: European journal of biochemistry 270 (2003), 6, S. 1065-1075 Institutsveröffentlichung: SCAI
  Abstract: NMR spectroscopy and X-ray crystallography have provided important insight into structural features of phenylalanine hydroxylase (PAH) and tyrosine hydroxylase (TH). Nevertheless, significant problems such as the substrate specificity of PAH and the different susceptibility of TH to feedback inhibition by l-3,4-dihydroxyphenylalanine (l-DOPA) compared with dopamine (DA) remain unresolved. Based on the crystal structures 5pah for PAH and 2toh for TH (Protein Data Bank), we have used molecular docking to model the binding of 6(R )-l-erythro-5,6,7,8-tetrahydrobiopterin (BH4 ) and the substrates phenylalanine and tyrosine to the catalytic domains of PAH and TH. The amino acid substrates were placed in positions common to both enzymes. The productive position of tyrosine in TH.BH4 was stabilized by a hydrogen bond with BH4 . Despite favorable energy scores, tyrosine in a position trans to PAH residue His290 or TH residue His336 interferes with the access of the essential cofactor dioxygen to the catalytic , thereby blocking the enzymatic reaction. DA and l-DOPA were directly coordinated to the active site iron via the hydroxyl residues of their catechol groups. Two alternative conformations, rotated 180degrees around an imaginary iron-catecholamine axis, were found for DA and l-DOPA in PAH and for DA in TH. Electrostatic forces play a key role in hindering the bidentate binding of the immediate reaction product l-DOPA to TH, thereby saving the enzyme from direct feedback inhibition. http://dx.doi.org/10.1046/j.1432-1033.2003.03429.x

• Öhsen, N. von; Sommer, I.; Zimmer, R.: Profile-Profile Alignment: A Powerful Tool for Protein Structure Prediction. In: Altman, R.B. (Hrsg.) u.a.: Pacific Symposium on Biocomputing 2003 : Kauai, Hawaii, 3 - 7 January 2003. Singapore : World Scientific Publishing, 2003, S. 252-263 Institutsveröffentlichung: SCAI: Abteilung: BIO Volltext externer Link

• Oosterlee, Cornelis W.: On multigrid for linear complementarity problems with application to American-style options. In: Electronic transactions on numerical analysis 15 (2003), S. 165-185 Institutsveröffentlichung: SCAI

• Post, Peter: MpCCI Version 2.0. In: Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 4th MpCCI User Forum : March 12th & 13th, 2003, Schloss Birlinghofen, Sankt augustin, Germany ; book of abstracts. Sankt Augustin : Fraunhofer SCAI, 2003, S. 4 Institutsveröffentlichung: SCAI

• Schwarz, Fritz; Gurski, V.; Samsonov, A.: Classical and non-classical symmetries for non-linear equations with dispersion and dissipation. In: Technical Physics. S. 1-5 Institutsveröffentlichung: SCAI

• Schwarz, Fritz: Symmetries of Second- and Third-Order Ordinary Differential Equations. In: Winkler, Franz (Hrsg.) u.a.: Symbolic and numerical scientific computation : second international conference, SNSC 2001, Hagenberg, Austria, September 12-14, 2001 ; revised papers. Berlin [u.a.] : Springer, 2003, S. 108-139 (Lecture notes in computer science 2630). Institutsveröffentlichung: SCAI: Abteilung: INA http://dx.doi.org/10.1007/3-540-45084-X%5F4 Volltext

• Sohler, Florian; Hanisch, Daniel; Zimmer, Ralf: New methods for joint analysis of biological networks and expression data. In: Oral presentations. München : Belleville-Verlag, 2003, S. 141-146 (Proceedings of the German Conference on Bioinformatics 2003 1). Institutsveröffentlichung: SCAI: Abteilung: ALG

• Sommer, Ingolf; Öhsen, Niklas von; Mevissen, Theo; Albrecht, Mario; Zimmer, Ralf; Lengauer, Thomas: The Arby automated protein structure prediction server. In: Spang, Rainer (Hrsg.) u.a.; Max-Planck-Institute for Molecular Genetics Berlin u.a.: Currents in computational molecular biology 2003 : RECOMB 2003, Berlin ; extended poster abstracts from the poster sessions. Berlin, 2003, S. 219-220 Schlagwörter: protein structure prediction; fold recognition; data flow engines Institutsveröffentlichung: SCAI

• Stueben, Klaus; Delaney, P.; Chmakow, S.: Algebraic Multigrid (AMG) for Ground Water Flow and Oil Reservoir Simulation. In: Proceedings of the Conference MODFLOW and More 2003: Understanding through Modeling (2003) Institutsveröffentlichung: SCAI: Abteilung: NUSO.AMG

• Thole, Clemens-August; Liquan, Mei: DIFF-CRASH - stability analysis in crash simulation. In: Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 4th MpCCI User Forum : March 12th & 13th, 2003, Schloss Birlinghofen, Sankt augustin, Germany ; book of abstracts. Sankt Augustin : Fraunhofer SCAI, 2003, S. 27 Institutsveröffentlichung: SCAI

• Trottenberg, Ulrich; Linden, Johannes: Simulation und Optimierung - Innovation durch Mathematik. In: Warnecke, Hans-Jürgen (Hrsg.) u.a.: Kunststück Innovation : Praxisbeispiele aus der Fraunhofer-Gesellschaft. Berlin [u.a.] : Springer, 2003, S. 55-60 Institutsveröffentlichung: SCAI

• Vet, Paul van der; Hofmann, Martin; Huibers, T.W.C.; Roosendaal, H.E.: Managing a portal of digital web resources by content syndication. In: Bra, P.M.E. de (Hrsg.): Conferentie Informatiewetenschap 2003 : Technische Universiteit Eindhoven 20 November 2003. Eindhoven : Technische Universiteit, 2003, S. 99-105 (Computer science report / Technische Universiteit Eindhoven 2003, 11). Institutsveröffentlichung: SCAI: Abteilung: BIO

• Wieder, P.; Ziegler, Wolfgang: Grid Scheduling Dictionary of Terms and Keywords. Global Grid Forum Documents, GFD-I.11, 2003 Institutsveröffentlichung: SCAI: Abteilung: WEB http://forge.gridforum.org/projects/ggf-editor/document/GFD-I.11/en/1/GFD-I.11.pdf

• Wolf, Klaus: A mapping tool for stamping and crash. In: Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 4th MpCCI User Forum : March 12th & 13th, 2003, Schloss Birlinghofen, Sankt augustin, Germany ; book of abstracts. Sankt Augustin : Fraunhofer SCAI, 2003, S. 22 Institutsveröffentlichung: SCAI

• Wolf, Klaus: Mesh-Explorer - tool box for multidisciplinary CAE data integration. In: Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 4th MpCCI User Forum : March 12th & 13th, 2003, Schloss Birlinghofen, Sankt augustin, Germany ; book of abstracts. Sankt Augustin : Fraunhofer SCAI, 2003, S. 20 Institutsveröffentlichung: SCAI

• Wolf, Klaus: MpCCI 2.x roadmap. In: Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 4th MpCCI User Forum : March 12th & 13th, 2003, Schloss Birlinghofen, Sankt augustin, Germany ; book of abstracts. Sankt Augustin : Fraunhofer SCAI, 2003, S. 6 Institutsveröffentlichung: SCAI

• Wolf, Klaus (Hrsg.); Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI Sankt Augustin: 4th MpCCI User Forum : March 12th & 13th, 2003, Schloss Birlinghofen, Sankt augustin, Germany ; book of abstracts. Sankt Augustin : Fraunhofer SCAI, 2003 Institutsveröffentlichung: SCAI

• Zien, Alexander; Fluck, Juliane; Zimmer, Ralf; Lengauer, Thomas: Microarrays: How Many Do You Need? In: Journal of computational biology 10 (2003), 3-4, S. 653-667 Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: We estimate the number of microarrays that is required in order to gain reliable results from a common type of study: the pairwise comparison of different classes of samples. We show that current knowledge allows for the construction of models that look realistic with respect to searches for individual differentially expressed genes and derive prototypical parameters from real data sets. Such models allow investigation of the dependence of the required number of samples on the relevant parameters: the biological variability of the samples within each class, the fold changes in expression that are desired to be detected, the detection sensitivity of the microarrays, and the acceptable error rates of the results. We supply experimentalists with general conclusions as well as a freely accessible Java applet at www.scai.fhg.de/special/bio/howmanyarrays/ for fine tuning simulations to their particular settings. http://dx.doi.org/doi:10.1089/10665270360688246

• Zimmermann, M.; Hindle, S.A.; Naumann, T.; Matter, H.; Hessler, G.; Baringhaus, K.H.; Lemmen, Christian; Gastreich, Marcus; Rarey, Matthias: HTSview - software which leads to lead ideas. In: 226th ACS National Meeting 2003 : abstract of papers. Washington, DC : ACS, 2003, S. 51 (Abstracts of papers of the American Chemical Society 226). Institutsveröffentlichung: SCAI

• Zimmermann, Marc; Rarey, Matthias; Naumann, T.; Matter, H.; Hessler, G.; Lengauer, Thomas: Extracting Knowledge from High-Throughput Screening Data: Towards the Generation of Biophore Models. In: Ford, M.G. (Hrsg.): EuroQSAR 2002 designing drugs and crop protectants: Processes, Problems and Solutions. Malden, mass. : Blackwell, 2003, S. 63-67 Institutsveröffentlichung: SCAI: Abteilung: BIO

2002

• Applications. Weinheim : Wiley-VCH, 2002 (Methods and principles in medicinal chemistry; 14) Institutsveröffentlichung: SCAI

• Basic technologies. Weinheim : Wiley-VCH, 2002 (Bioinformatics; 1) Institutsveröffentlichung: SCAI

• Aigner, Thomas; Bartnik, E.; Zien, Alexander; Zimmer, Ralf: Functional genomics of osteoarthritis. In: Pharmacogenomics 3 (2002), 5, S. 635-650 Institutsveröffentlichung: SCAI
  Abstract: Functional genomics is a challenging new way to address a complex disease like osteoarthritis on a molecular level. Despite osteoarthritis being ultimately a biochemical problem, mainly characterized by an imbalanced cartilage matrix turnover, a deeper understanding of molecular events within the tissue cells (i.e., the chondrocytes) will provide not only a better understanding of pathogenetic mechanisms but also new diagnostic markers and cellular targets for therapeutic intervention. This innovative technology represents a challenging approach complementing (not replacing) classical research in previously described and new disease-relevant genes: large-scale functional genomics will open up new areas of so far unrecognized molecular networks. This will include as yet unidentified players in the anabolicScatabolic balance of matrix turnover of articular cartilage as well as disease-relevant intracellular signaling cascades so far hardly investigated in articular chondrocytes. However, care must be taken not to over or misinterpret results and some major challenges must be overcome in order to properly utilize the potential of this technology in the field of osteoarthritis.
  http://dx.doi.org/10.1517/14622416.3.5.635

• Aigner, Thomas; Finger, F.; Gebhard, Pia Margarethe; Zien, Alexander; Zimmer, R.: Genexpressionsprofilierung adulter humaner Chondrozyten mittels der cDNA-Array-Technologie. In: Zeitschrift für Rheumatologie 61 (2002), 3, S. 260-262 Institutsveröffentlichung: SCAI http://dx.doi.org/10.1007/s00393-002-0406-6

• Albrecht, M.; Hanisch, Daniel; Zimmer, Ralf; Lengauer, Thomas: Improving fold recognition of protein threading by experimental distance constraints. In: In silico biology 2 (2002), 3, S. 325-337 Institutsveröffentlichung: SCAI: Abteilung: BIO

• Beerenwinkel, Nico; Schmidt, Barbara; Walter, Hauke; Kaiser, Rolf; Lengauer, Thomas; Hoffmann, Daniel; Korn, Klaus; Selbig, Joachim: Diversity and complexity of HIV-1 drug resistance : a bioinformatics approach to predicting phenotype from genotype. In: Proceedings of the National Academy of Sciences of the United States of America 99 (2002), 12, S. 8271-8276 Institutsveröffentlichung: SCAI
  Abstract: Drug resistance testing has been shown to be beneficial for clinical management of HIV type 1 infected patients. Whereas phenotypic assays directly measure drug resistance, the commonly used genotypic assays provide only indirect evidence of drug resistance, the major challenge being the interpretation of the sequence information. We analyzed the significance of sequence variations in the protease and reverse transcriptase genes for drug resistance and derived models that predict phenotypic resistance from genotypes. For 14 antiretroviral drugs, both genotypic and phenotypic resistance data from 471 clinical isolates were analyzed with a machine learning approach. Information profiles were obtained that quantify the statistical significance of each sequence position for drug resistance. For the different drugs, patterns of varying complexity were observed, including between one and nine sequence positions with substantial information content. Based on these information profiles, decision tree classifiers were generated to identify genotypic patterns characteristic of resistance or susceptibility to the different drugs. We obtained concise and easily interpretable models to predict drug resistance from sequence information. The prediction quality of the models was assessed in leave-one-out experiments in terms of the prediction error. We found prediction errors of 9.6-15.5% for all drugs except for zalcitabine, didanosine, and stavudine, with prediction errors between 25.4% and 32.0%. http://dx.doi.org/10.1073/pnas.112177799

• Bendisch, Jürgen; Reimann, S.; Trotha, Hartmut von: Site percolation for a class of constrained honeycomb lattices. In: Physica / A, Statistical mechanics and its applications 307 (2002), 1-2, S. 1-14 Schlagwörter: site percolation; constrained honeycomb lattice; natural process; correlated random media; randomly bicolored triangular lattice; local constraint; spontaneous magnetization; critical concentration; groundstate; Random; stochastic independence Institutsveröffentlichung: SCAI
  Abstract: We consider site percolation in a class of correlated random media derived from randomly bi-colored triangular lattices. Media are constructed due to specific state-dependent local constraints. Constraints destroy stochastic independence of elementary events and have specific impact on site percolation thresholds. Further, a connection to critical concentrations of spontaneous magnetization in random 2D+or-J Ising models, at groundstates, is discussed. http://dx.doi.org/10.1016/S0378-4371(01)00611-2

• Benkner, Siegfried; Brandes, Thomas: Efficient Parallel Programming on Scalable Shared Memory Systems with High Performance Fortran. In: Concurrency and computation (2002), S. 789-803 Institutsveröffentlichung: SCAI: Abteilung: NUSO

• Durchholz, Reiner: A generic causal model for place latency. In: Theoretical computer science / A u. B 289 (2002), 1, S. 1-49 Institutsveröffentlichung: SCAI
  Abstract: For a prototypical class of time-extended Petri nets it is shown that the extension does not increase their expressive power. The nets in this class have token latencies attributed to places. Place latency nets are formally defined together with their firing semantics. For any place latency system, an explicit construction of an elementary net system is given as an implementation, which is proven to be behaviourally equivalent. The adequacy problem of deciding which equivalence notion to apply is moderated by the fact that the implementation satisfies the B-condition, under which all better known equivalence notions coincide. http://dx.doi.org/10.1016/S0304-3975(01)00327-9

• Eggeling, Eva; Ta´asan, Shlomo: An optimization algorithm for the meteorological data assimilation problem. In: Chan, T.F. (Hrsg.) u.a.: Recent progress in computational and applied PDES : conference proceedings for the international conference held in Zhangjiajie in July 2001. New York, NY [u.a.] : Kluwer Academic/Plenum Publishers, 2002, S. 171-181 Institutsveröffentlichung: SCAI

• Freudenberg, J.; Hanisch, Daniel; Zimmer, Ralf; Lengauer, Thomas: A hypergraph-based method for unification of existing protein structure- and sequence-families. In: In silico biology 2 (2002), 31, S. 339-349 Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Classification of proteins is a major challenge in bioinformatics. Here an approach is presented, that unifies different existing classifications of protein structures and sequences. Protein structural domains are repre-sented as nodes in a hypergraph. Shared memberships in sequence families result in hyperedges in the graph. The presented method partitions the hypergraph into clusters of structural domains. Each computed cluster is based on a set of shared sequence family memberships. Thus, the clusters put existing protein sequence families into the context of structural family hierarchies. Conversely, structural domains are related to their sequence family member-ships, which can be used to gain further knowledge about the respective structural families.

• Fuellenbach, Tanja; Stuebe, Klaus: Algebraic multigrid for selected PDE systems. In: Bemelmans, Josef (Hrsg.) u.a.: Elliptic and parabolic problems : proceedings of the 4th European conference, Rolduc, Netherlands, 18-22 June 2001, Gaeta, Italy, 24-28 September 2001. New Jersey, NJ [u.a.] : World Scientific, 2002 Institutsveröffentlichung: SCAI: Abteilung: NUSO

• Füllenbach, Tanja: Algebraic multigrid for selected systems of partial differential equations : Forschungsbericht, Graduiertenkolleg Scientific Computing 4/2001 - 3/2002. Köln : Universität Köln, 2002 Institutsveröffentlichung: SCAI: Abteilung: NUSO

• Hanisch, Daniel; Zien, Alexander; Zimmer, Ralf; Lengauer, Thomas: Co-clustering of biological networks and gene expression data. In: Bioinformatics (2002), S. 145-154 Institutsveröffentlichung: SCAI: Abteilung: ALG

• Hanisch, Daniel; Zimmer, Ralf; Lengauer, Thomas: ProML - the Protein Markup Language for specification of protein sequences. In: In silico biology 2 (2002), 3, S. 313-324 Institutsveröffentlichung: SCAI: Abteilung: BIO

• Hindle, S.A.; Rarey, Matthias; Buning, Christian; Lengauer, Thomas: Flexible docking under pharmacophore type constraints. In: Journal of computer-aided molecular design 16 (2002), 2, S. 129-149 Institutsveröffentlichung: SCAI
  Abstract: FlexX-Pharm, an extended version of the flexible docking tool FlexX, allows the incorporation of information about important characteristics of protein-ligand binding modes into a docking calculation. This information is introduced as a simple set of constraints derived from receptor-based type pharmacophore features.
  The constraints are determined by selected FlexX interactions and inclusion volumes in the receptor active site. They guide the docking process to produce a set of docking solutions with particular properties. By applying a series of look-ahead checks during the flexible construction of ligand fragments within the active site, FlexX-Pharm determines which partially built docking solutions can potentially obey the constraints. Solutions that will not obey the constraints are deleted as early as possible, often decreasing the calculation time and enabling new docking solutions to emerge. FlexX-Pharm was evaluated on various individual protein-ligand complexes where the top docking solutions generated by FlexX had high root mean square deviations (RMSD) from the experimentally observed binding modes. FlexX-Pharm showed an improvement in the RMSD of the top solutions in most cases, along with a reduction in run time. We also tested FlexX-Pharm as a database screening tool on a small dataset of molecules for three target proteins. In two cases, FlexX-Pharm missed one or two of the active molecules due to the constraints selected. However, in general FlexX-Pharm maintained or improved the enrichment shown with FlexX, while completing the screen in considerably less run time. http://dx.doi.org/10.1023/A:1016399411208

• Hoffmann, Daniel; Schnaible, Volker; Wefing, Stephan; Albrecht, Mario; Hanisch, Daniel; Zimmer, Ralf: A new method for the fast solution of protein-3D-Structures, combining experiments- and bioinformatics. In: Hoffmann, Karl-Heinz (Hrsg.): Coupling of biological and electronic systems : proceedings of the 2nd Caesarium, Bonn, November 1 - 3, 2000. Berlin [u.a.] : Springer, 2002, S. 59-78 Institutsveröffentlichung: SCAI

• Hotzel, Eckehart: Right projective semigroups with 0. In: Journal of pure and applied algebra 170 (2002), 1, S. 35-66 Institutsveröffentlichung: SCAI: Abteilung: ALG.CADE http://dx.doi.org/10.1016/S0022-4049(01)00070-6

• Jakumeit, Jürgen; Ravaioli, Umberto: Influence of electron-electron scattering on the hot electron distribution in ultra-short Si-MOSFETs. In: Physica / B, Condensed matter 314 (2002), 1-4, S. 363-366 Institutsveröffentlichung: SCAI
  Abstract: The influence of electronSelectron scattering on the hot electron distribution in Si-MOSFETs with channel length down to 25 nm is investigated using the local iterative Monte Carlo (LIMO) technique. The LIMO approach simplifies the calculation of electronSelectron scattering since the electron distribution is accessible throughout the simulation. An excellent agreement with available experimental findings could be achieved. Our results indicate that the heating of electrons becomes less pronounced for channel length below 50 nm due to a more ballistic electron transport through the channel. http://dx.doi.org/10.1016/S0921-4526(01)01426-0

• Klawonn, Axel; Widlund, O.B.; Dryja, M.: Dual-Primal FETI Methods for Three-Dimensional Elliptic Problems with Heterogeneous Coefficients. In: SIAM journal on numerical analysis 40 (2002), 1, S. 159-179 Institutsveröffentlichung: SCAI http://dx.doi.org/10.1137/S0036142901388081

• Klawonn, Axel; Widlund, Olof B.; Dryja, Maksymilian: Dual-Primal FETI Methods with Face Constraints. In: Pavarino, Luca F. (Hrsg.) u.a.: Recent developments in domain decomposition methods : Workshop on Domain Decomposition helt at ETH, Zürich on June 7-8th, 2001. Berlin [u.a.] : Springer, 2002, S. 27-40 (Lecture notes in computational science and engineering 23). Institutsveröffentlichung: SCAI

• Kleinschmidt, Martin; Tatchen, Jörg; Marian, Christel M.: Spin-orbit coupling of DFT/MRCI wavefunctions : method, test calculations, and application to Thiophene. In: Journal of computational chemistry 23 (2002), 8 : Special issue, S. 824-833 Institutsveröffentlichung: SCAI http://dx.doi.org/10.1002/jcc.10064

• Lengauer, Thomas: From Genomes to Drugs with Bioinformatics. In: Basic technologies. Weinheim : Wiley-VCH, 2002, S. 3-25 (Bioinformatics 1). Institutsveröffentlichung: SCAI

• Lengauer, Thomas: Future Trends. In: Applications. Weinheim : Wiley-VCH, 2002, S. 171-187 (Methods and principles in medicinal chemistry 14). Institutsveröffentlichung: SCAI

• Lengauer, Thomas: Glossary of algorithmic terms in bioinformatics. In: Basic technologies. Weinheim : Wiley-VCH, 2002, S. 405-424 (Bioinformatics 1). Institutsveröffentlichung: SCAI

• ECCB 2002 Lengauer, Thomas (Hrsg.) u.a.: Bioinformatics 18 (2002), Supplement 2 Oxford [u.a.] : Oxford University Press Institutsveröffentlichung: SCAI: Abteilung: ALG

• Selected papers from RECOMB 2001 Lengauer, Thomas (Hrsg.): Journal of computational biology 9 (2002), 2 New York, NY : Liebert ISSN 1066-5277 Institutsveröffentlichung: SCAI: Abteilung: ALG

• Li, Ziming; Schwarz, Fritz; Tsarev, Serguei P.: Factoring Zero-dimensional Ideals of Linear Partial Differential Operators. In: Mora, Teo (Hrsg.): ISSAC 2002 : proceedings of the 2002 ACM-SIGSAM International Symposium on Symbolic and Algebraic Computation, July 07-10, 2002, Université de Lille, Lille, France. New York, NY : ACM, 2002, S. 168-175 Institutsveröffentlichung: SCAI http://portal.acm.org/citation.cfm?doid=780506.780528

• Linden, Johannes (Red.); Krapp, Michael (Red.); Ehling, Susanne (Red.); Maskell, Barbara (Red.): Jahresbericht 2001 / Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI. Sankt Augustin : Fraunhofer SCAI, 2002 (Jahresbericht / Fraunhofer-Institut Algorithmen und Wissenschaftliches Rechnen SCAI) Institutsveröffentlichung: SCAI Volltext

• Motherwell, W.D.S.; Ammon, Herman L.; Dunitz, Jack D.; Dzyabchenko, A.; Erk, P.; Gavezzotti, A.; Hofmann, D.W.M.; Leusen, F.J.J.; Lommerse, J.P.M.; Mooij, W.T.M.; Price, S.L.; Scheraga, H.; Schweizer, B.; Schmidt, M.U.; Eijck, B.P. van; Verwer, P.; Williams, D.E.: Crystal structure prediction of small organic molecules: A second blind test. In: Acta crystallographica / Section B, Structural science 58 (2002), 4, S. 647-661 Institutsveröffentlichung: SCAI
  Abstract: The first collaborative workshop on crystal structure prediction (CSP1999) has been followed by a second workshop (CSP2001) held at the Cambridge Crystallographic Data Centre. The 17 participants were given only the chemical diagram for three organic molecules and were invited to test their prediction programs within a range of named common space groups. Several different computer programs were used, using the methodology wherein a molecular model is used to construct theoretical crystal structures in given space groups, and prediction is usually based on the minimum calculated lattice energy. A maximum of three predictions were allowed per molecule. The results showed two correct predictions for the first molecule, four for the second molecule and none for the third molecule (which had torsional flexibility). The correct structure was often present in the sorted low-energy lists from the participants but at a ranking position greater than three. The use of non-indexed powder diffraction data was investigated in a secondary test, after completion of the ab initio submissions. Although no one method can be said to be completely reliable, this workshop gives an objective measure of the success and failure of current methodologies. http://dx.doi.org/10.1107/S0108768102005669

• Oosterlee, Cornelis W.; Wienands, Roman: A genetic search for optimal multigrid components within a Fourier analysis setting. In: SIAM journal on scientific computing 24 (2002), 3, S. 924-944 Institutsveröffentlichung: SCAI
  Abstract: In this paper, Fourier analysis is used for finding efficient multigrid components. The individual multigrid components for several discrete partial differential operators are chosen automatically by a genetic optimization method. From a set of multigrid components, such as different smoothers, coarse grid correction components, cycle types, number of smoothing iterations, and relaxation parameters, an optimal three-grid Fourier convergence factor corrected for computational complexity is obtained by the genetic search. The resulting methods can be tuned for optimal efficiency or toward robustness. The analysis results are verified by numerical experiments. http://dx.doi.org/10.1137/S1064827501397950

• Post, Peter; Schilcher, K.: Kl3 form factors at order p6 of chiral perturbation theory. In: The European physical journal / C, Particles and fields 25 (2002), 3, S. 427-443 Institutsveröffentlichung: SCAI: Abteilung: SIAN http://dx.doi.org/10.1007/s10052-002-0967-1

• Rarey, Matthias: Protein-Ligand Docking in Drug Design. In: Basic technologies. Weinheim : Wiley-VCH, 2002, S. 315-360 (Bioinformatics 1). Institutsveröffentlichung: SCAI

• Reinhardt, S.; Gastreich, M.; Marian, Christel Maria: Quantum Chemical Investigation of Initial Reactions between the Molecular Precursor TADB and Ammonia. I: Gas-Phase reactions. In: The journal of physical chemistry / A, Molecules, spectroscopy, kinetics, environment & general theory 106 (2002), 16, S. 4205-4216 Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Cl3Si(NH)BCl2, i.e., [(trichlorosilyl)amino]dichloroborane or TADB may act as a molecular precursor in syntheses to high-demand Si/B/N ceramics. To build a ceramic such as Si3B3N7. one may use liquid ammonia as the network forming agent. The actual processes which lead to such amorphous material are not yet fully understood. With this work. we aim at a quantification of product formation probabilities during initial reactions of TADB with NH3. For this reason, we have investigated the less complicated case of various gas-phase reactions with perturbation theory, and the situation in the liquid phase Will be published separately, In more detail, the reactions comprise (a) the first and second ammonolysis of TADB, (b) the decomposition of adducts (H3N --> SiCl3NHBCl2 and H3N --> BCl2NHSiCl3.). (c) the dimerization of TADB, and finally (d) a continuing reaction of TADB with the most probable product of the first ammonolysis of TADB (which we term TACBA, trichlorosilylaminochloroboryl amine). Besides these initial steps. and because of the significance of their products, reactions of TACBA with other TACBA molecules and formations of borazine derivates have also been looked into. Our results confirm qualitative chemical intuition: The major primary process in the gas phase is a substitution at the boron of TADB to yield TACBA. Also. it can be seen that the dissociation of the H3N --> BCl2NHSiCl3 adduct into BCl2NH2 and SiCl3NH2 is a side reaction. Albeit, in the continuing stage, the trimerization of TACBA under formation of a borazane six-membered ring releases much more energy than competing processes and is therewith important. As further reactions to be taken into consideration, we find a branching of the molecular backbone accompanied by a break-up of the Si-N-B unit in TADB and a second ammonolysis at the boron side of TACBA. Linking monomer units becomes energetically less and less probable as the ammonolyses of Si-Cl and B-Cl bonds proceed.

• Schwarz, Fritz: ALLTYPES: An Algebraic Language and Type System. In: Cohen, A.M. (Hrsg.) u.a.: Mathematical software : Proceedings of the first international congress of mathematical software, Beijing, China 17 - 19 August 2002. Singapore : World Scientific, 2002, S. 486-500 Institutsveröffentlichung: SCAI

• Schwarz, Fritz: Equivalence Classes, Symmetries and Solutions of Linear Third Order Differential Equations. In: Computing 69 (2002), S. 140-162 Institutsveröffentlichung: SCAI
  Abstract: The subject of this article are third-order differential equations that may be linearized by a variable change. To this end, at first the equivalence classes of linear equations are completely described. Thereafter it is shown how they combine into symmetry classes that are determined by the various symmetry types. An algorithm is presented allowing it to transform linearizable equations by hyperexponential transformations into linear form from which solutions may be obtained more easily. Several examples are worked out in detail.
  http://dx.doi.org/10.1007/s00607-002-1454-0

• Sommer, Ingolf; Zien, Alexander; Öhsen, Niklas von; Zimmer, Ralf; Lengauer, Thomas: Confidence Measures for Protein Fold Recognition. In: Bioinformatics 18 (2002), 6, S. 802-812 Institutsveröffentlichung: SCAI: Abteilung: BIO
  Abstract: Motivation: We present an extensive evaluation of different methods and criteria to detect remote homologs of a given protein sequence. We investigate two associated problems: first, to develop a sensitive searching method to identify possible candidates and, second, to assign a confidence to the putative candidates in order to select the best one. For searching methods where the score distributions are known, p-values are used as confidence measure with great success. For the cases where such theoretical backing is absent, we propose empirical approximations to p-values for searching procedures. Results: As a baseline, we review the performances of different methods for detecting remote protein folds (sequence alignment and threading, with and without sequence profiles, global and local). The analysis is performed on a large representative set of protein structures. For fold recognition, we find that methods using sequence profiles generally perform better than methods using plain sequences, and that threading methods perform better than sequence alignment methods. In order to assess the quality of the predictions made, we establish and compare several confidence measures, including raw scores, Z-scores, raw score gaps, z-score gaps, and different methods of p-value estimation. We work our way from the theoretically well backed local scores towards more explorative global and threading scores. The methods for assessing the statistical significance of predictions are compared using specificity-sensitivity plots. For local alignment techniques we find that p-value methods work best, albeit computationally cheaper methods such as those based on score gaps achieve similar performance. For global methods where no theory is available methods based on score gaps work best. By using the score gap functions as the measure of confidence we improve the more powerful fold recognition methods for which p-values are unavailable. http://dx.doi.org/10.1093/bioinformatics/18.6.802

• Sprengel, Frauke: Comparing multilevel coarsening strategies. In: Electronic transactions on numerical analysis 14 (2002), S. 178-194 Schlagwörter: multilevel coarsening strategy; subspace splitting; elliptic boundary value problem; finite element; boundary-value problem Institutsveröffentlichung: SCAI
  Abstract: We compare several multilevel coarsening strategies by using stable subspace splitting techniques. The obtained condition numbers give an answer on how well the coarsening strategies are suited for solving an anisotropic elliptic boundary value problem.

• Sthal, Martin; Rarey, Matthias; Klebe, Gerhard: Screening of Drug Databases. In: Applications. Weinheim : Wiley-VCH, 2002, S. 137-170 (Methods and principles in medicinal chemistry 14). Institutsveröffentlichung: SCAI

• Stüben, Klaus: Scalable Solvers for Sparse Linear Systems. In: ERCIM News (2002), 50 Institutsveröffentlichung: SCAI Volltext externer Link

• Wickert, L.; Selbig, Joachim: Structural analysis of the DNA-binding domain of alternatively spliced steroid receptors. In: The journal of endocrinology 173 (2002), 3, S. 429-436 Institutsveröffentlichung: SCAI
  Abstract: We have generated 24 DNA-binding domain structure models of alternatively spliced or mutated steroid receptor variants by homology-based modeling. Members of the steroid receptor family dispose of a DNA-binding domain which is built from two zinc fingers with a preserved sequence homology of about 90%. Data from crystallographic analysis of the glucocorticoid receptor DNA-binding domain are therefore appropriate to serve as a template structure. We inserted or deleted amino acid residues in order to study the structural details of the glucocorticoid, mineralocorticoid, and androgen receptor splice variants. The receptor variants are created by QUANTA- and MODELLER-based modeling. Subsequently, the resulting energy-minimized models were compared with each other and with the wild-type receptor respectively. A prediction for the receptor function based mainly on the preservation or destruction of secondary structures has been carried out. The simulations showed that amino acid insertions of one, four or nine additional residues of existing steroid receptor splice variants were tolerated without destruction of the secondary structure. In contrast, a deletion of four amino acids at the splice site junction leads to modifications in the secondary structure of the DNA-recognition helix which apparently disturb the receptor-DNA interaction. Furthermore, an insertion of 23 amino acid residues between the zinc finger of the androgen receptor leads to a large loop with an additional a-helical structure which seems to disconnect a specific contact from its hormone response element. Thereafter, the prediction of receptor function based on the molecular models was compared with the available experimental results from the in vitro function tests. We obtained a close correspondence between the molecular modeling-based predictions and the conclusions of receptor function drawn from in vitro studies. http://dx.doi.org/10.1677/joe.0.1730429

• Zien, Alexander; Fluck, Juliane; Zimmer, Ralf; Lengauer, Thomas: Microarrays: How Many Do You Need? In: Myers, Gene (Hrsg.) u.a.; Association for Computing Machinery: RECOMB 2002 : proceedings of the sixth annual International Conference on Computational Molecular Biology, April 18-21, 2002, Washington, DC, USA. New York, NY : ACM Press, 2002, S. 321-330 Institutsveröffentlichung: SCAI: Abteilung: ALG.BEX http://doi.acm.org/10.1145/565196.565239

• Zimmer, Ralf; Lengauer, Thomas: Protein Structure Prediction. In: Basic technologies. Weinheim : Wiley-VCH, 2002, S. 237-313 (Bioinformatics 1). Institutsveröffentlichung: SCAI