Extreme high demands on designing accurate prototypes for example in the fields of medical research, aircraft construction, shipbuilding and automotive industry require multidisciplinary simulations. A large number of...
Extreme high demands on designing accurate prototypes for example in the fields of medical research, aircraft construction, shipbuilding and automotive industry require multidisciplinary simulations. A large number of tools for monodisciplinary simulations are available today. Each of these provides high quality simulation results in a specific physical domain. Now there is also a solution to do multidisciplinary computations: Parallel monodisciplinary codes are coupled with the Mesh based parallel Code Coupling Interface MpCCI to solve multidisciplinary problems with a loose coupled approach. The paper presents applications in the framework of fluid-structure interaction, which demonstrate the advantages of the parallel coupling library for this kind of problems. The computational fluid dynamics code FLOWer developed at the institute of Design Aerodynamics/DLR and the structural mechanics code SIMPACK developed at the institute of Aeroelasticity/DLR are coupled to solve an aeroelastic test problem. The applicability of the coupling library in the field of aeroelasticity is strongly dependent on the integrated interpolations between the involved meshes. In the institute of Aeroelasticity the aeroelastic analysis tool CAESAR was developed which includes aeroelasticity specific interpolation algorithms. These routines are integrated in MpCCI via a special interface. There are two types of interpolation routines included. The first kind of algorithms is based on the method of finite interpolation elements and the second uses radial basis functions.
MOTIVATION:Large scale gene expression data are often analysed by clustering genes based on gene expression data alone, though a priori knowledge in the form of biological networks is available. The use of this additi...
MOTIVATION:Large scale gene expression data are often analysed by clustering genes based on gene expression data alone, though a priori knowledge in the form of biological networks is available. The use of this additional information promises to improve exploratory analysis considerably.
RESULTS:We propose constructing a distance function which combines information from expression data and biological networks. Based on this function, we compute a joint clustering of genes and vertices of the network. This general approach is elaborated for metabolic networks. We define a graph distance function on such networks and combine it with a correlation-based distance function for gene expression measurements. A hierarchical clustering and an associated statistical measure is computed to arrive at a reasonable number of clusters. Our method is validated using expression data of the yeast diauxic shift. The resulting clusters are easily interpretable in terms of the biochemical network and the gene expression data and suggest that our method is able to automatically identify processes that are relevant under the measured conditions.
We present a comprehensive analysis of methods for improving the fold recognition rate of the threading approach to protein structure prediction by the utilization of few additional distance constraints. The distance ...
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We present a comprehensive analysis of methods for improving the fold recognition rate of the threading approach to protein structure prediction by the utilization of few additional distance constraints. The distance constraints between protein residues may be obtained by experiments such as mass spectrometry or NMR spectroscopy. We applied a post-filtering step with new scoring functions incorporating measures of constraint satisfaction to ranking lists of 123D threading alignments. The detailed analysis of the results on a small representative benchmark set show that the fold recognition rate can be improved significantly by up to 30% from about 54%-65% to 77%-84%, approaching the maximal attainable performance of 90% estimated by structural superposition alignments. This gain in performance adds about 10% to the recognition rate already achieved in our previous study with cross-link constraints only. Additional recent results on a larger benchmark set involving a confidence function for threading predictions also indicate notable improvements by our combined approach, which should be particularly valuable for rapid structure determination and validation of protein models.
The paper describes TENT, a component-based framework for the integration of technical applications. TENT allows the engineer to design, automate, control, and steer technical workflows interactively. The applications...
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Alignments of frequency profiles against frequency profiles have a wide scope of applications in currently used bioinformatic analysis tools ranging from multiple alignment methods based on the progressive alignment a...
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The ever increasing number of experimentally resolved crystal structures supports the possibility of fully empirical crystal structure prediction for small organic molecules. Empirical methods promise to be significan...
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Microarrays measure values that are approximately proportional to the numbers of copies of different mRNA molecules in samples. Due to technical difficulties, the constant of proportionality between the measured inten...
Along the long path from genomic data to a new drug, the knowledge of three-dimensional protein structure can be of significant help in several *** paper points out such places, discusses the virtues of protein struct...
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Along the long path from genomic data to a new drug, the knowledge of three-dimensional protein structure can be of significant help in several *** paper points out such places, discusses the virtues of protein structure knowledge and reviews bioinformatics methods for gaining such knowledge on the protein structure.
In the AMANDA project a component-based framework for the integration of coupled technical applications, running distributed in a network, is developed. It is designed to deal with parallel and sequential programs and...
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