Michael Lenke

Bio: Michael Lenke is an academic researcher from Technische Universität München. The author has contributed to research in topics: Solver & Fortran. The author has an hindex of 2, co-authored 5 publications receiving 6578 citations.

ARB: a software environment for sequence data

Abstract: The ARB (from Latin arbor, tree) project was initiated almost 10 years ago. The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface. Although it was initially designed for ribosomal RNA data, it can be used for any nucleic and amino acid sequence data as well. A central database contains processed (aligned) primary structure data. Any additional descriptive data can be stored in database fields assigned to the individual sequences or linked via local or worldwide networks. A phylogenetic tree visualized in the main window can be used for data access and visualization. The package comprises additional tools for data import and export, sequence alignment, primary and secondary structure editing, profile and filter calculation, phylogenetic analyses, specific hybridization probe design and evaluation and other components for data analysis. Currently, the package is used by numerous working groups worldwide.

Dataparallel implicit Navier–Stokes solver on different multiprocessors

Abstract: Publisher Summary This chapter discusses the parallelization of a Navier–Stokes solver on the multiprocessors of different architectures and programming models, a system with shared memory, and several systems with distributed-memory. For communication, all multiprocessors use a message based model and are reproduced on the multiprocessor architecture by means of available communication models. This is done in such a way that only a machine specific interface has to be exchanged. The results obtained by the parallel Navier–Stokes solver on multiprocessor systems (transonic flow around a profile) are compared with those of workstations and super vector computers. The developed communication model has proofed as a flexible, reliable, and efficient implementation. High speed-ups are obtained on any multiprocessor because there are workstation clusters or massive parallel systems. It allows the computation of a wide range of block-structured grids and is easily transferable.

Big Computations with a 3-D Parallel Navier-Stokes Solver on Different Multiprocessors

Abstract: The practical use of massive parallel systems includes the computation of big 3-D fluid dynamic problems, which require a large amount of main memory.

NSFLEX90 — A 3d Euler and Navier-Stokes Solver in Fortran 90

Abstract: FORTRAN (FORmula TRANslation) is the principle language used in fields of scientific, numerical, and engineering programming. On the one hand it requires much less computer science knowledge by the programmer than other languages, and it is much easier to use. On the other hand fast object code can be generated, which is very important for scientific, numerical and engineering applications. Therefore, on almost every computer system compilers with preprocessors are available for that language.

On the Performance Enhancements of a CFD Algorithm in High Performance Computing

Abstract: This report deals with aspects concerning HPC with respect to the industrial CFD solver NSFLEX for aerodynamic problems. Since 1992, this solver has been parallelized and tested on different parallel computer architectures and different communication paradigms. Good performance results could be achieved. Based on that parallel solver, some more aspect are considered in this report to improve its performance behavior. Multigrid techniques and cg-like methods are implemented as well as the use of new programming paradigms like Fortran 90 and HPF (High Performance Fortran). Again, performance improvement can be achieved. Furthermore, one very important aspect concerning the application cycle of high parallel solvers is introduced and an interactive tool concept is proposed which enables online monitoring, online analyzing and online steering of parallel simulations to the user.

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Abstract: SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Abstract: mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the alpha and beta diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

Abstract: A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.

UniFrac: a New Phylogenetic Method for Comparing Microbial Communities

Abstract: We introduce here a new method for computing differences between microbial communities based on phylogenetic information. This method, UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but not both. UniFrac can be used to determine whether communities are significantly different, to compare many communities simultaneously using clustering and ordination techniques, and to measure the relative contributions of different factors, such as chemistry and geography, to similarities between samples. We demonstrate the utility of UniFrac by applying it to published 16S rRNA gene libraries from cultured isolates and environmental clones of bacteria in marine sediment, water, and ice. Our results reveal that (i) cultured isolates from ice, water, and sediment resemble each other and environmental clone sequences from sea ice, but not environmental clone sequences from sediment and water; (ii) the geographical location does not correlate strongly with bacterial community differences in ice and sediment from the Arctic and Antarctic; and (iii) bacterial communities differ between terrestrially impacted seawater (whether polar or temperate) and warm oligotrophic seawater, whereas those in individual seawater samples are not more similar to each other than to those in sediment or ice samples. These results illustrate that UniFrac provides a new way of characterizing microbial communities, using the wealth of environmental rRNA sequences, and allows quantitative insight into the factors that underlie the distribution of lineages among environments.

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

Abstract: Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification of microbial diversity. The ARB software suite with its corresponding rRNA datasets has been accepted by researchers worldwide as a standard tool for large scale rRNA analysis. However, the rapid increase of publicly available rRNA sequence data has recently hampered the maintenance of comprehensive and curated rRNA knowledge databases. A new system, SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains. All sequences are checked for anomalies, carry a rich set of sequence associated contextual information, have multiple taxonomic classifications, and the latest validly described nomenclature. Furthermore, two precompiled sequence datasets compatible with ARB are offered for download on the SILVA website: (i) the reference (Ref) datasets, comprising only high quality, nearly full length sequences suitable for in-depth phylogenetic analysis and probe design and (ii) the comprehensive Parc datasets with all publicly available rRNA sequences longer than 300 nucleotides suitable for biodiversity analyses. The latest publicly available database release 91 (August 2007) hosts 547 521 sequences split into 461 823 small subunit and 85 689 large subunit rRNAs.