Biomedical subjects

Jan Krüger

Publications and source records attributed to Jan Krüger.

6 recordsLinked to original sources

PubMed2006

XML schemas for common bioinformatic data types and their application in workflow systems.

BACKGROUND: Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data--therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. RESULTS: Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at http://bioschemas.sourceforge.net, the BioDOM library can be obtained at http://biodom.sourceforge.net. CONCLUSION: The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios.

Algorithms↗

PubMed2006

RNAhybrid: microRNA target prediction easy, fast and flexible.

In the elucidation of the microRNA regulatory network, knowledge of potential targets is of highest importance. Among existing target prediction methods, RNAhybrid [M. Rehmsmeier, P. Steffen, M. Höchsmann and R. Giegerich (2004) RNA, 10, 1507-1517] is unique in offering a flexible online prediction. Recently, some useful features have been added, among these the possibility to disallow G:U base pairs in the seed region, and a seed-match speed-up, which accelerates the program by a factor of 8. In addition, the program can now be used as a webservice for remote calls from user-implemented programs. We demonstrate RNAhybrid's flexibility with the prediction of a non-canonical target site for Caenorhabditis elegans miR-241 in the 3'-untranslated region of lin-39. RNAhybrid is available at http://bibiserv.techfak.uni-bielefeld.de/rnahybrid.

3' Untranslated Regions↗

PubMed2004

e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences.

e2g is a web-based server which efficiently maps large expressed sequence tag (EST) and cDNA datasets to genomic DNA. It significantly extends the volume of data that can be mapped in reasonable time, and makes this improved efficiency available as a web service. Our server hosts large collections of EST sequences (e.g. 4.1 million mouse ESTs of 1.87 Gb) in precomputed indexed data structures for efficient sequence comparison. The user can upload a genomic DNA sequence of interest and rapidly compare this to the complete collection of ESTs on the server. This delivers a mapping of the ESTs on the genomic DNA. The e2g web interface provides a graphical overview of the mapping. Alignments of the mapped EST regions with parts of the genomic sequence are visualized. Zooming functions allow the user to interactively explore the results. Mapped sequences can be downloaded for further analysis. e2g is available on the Bielefeld University Bioinformatics Server at http://bibiserv.techfak.uni-bielefeld.de/e2g/.

Base Sequence↗

PubMed2004

A low-volume platform for cell-respirometric screening based on quenched-luminescence oxygen sensing.

Cell viability assays represent an important technology in modern cell biology, drug discovery and biotechnology, where currently there is a high demand for simple, sensitive and cost-effective screening methods. We have developed a new methodology and associated tools for cell-based screening assays, which are based on the measurement of the rates of oxygen uptake in cells by luminescence quenching. Sealable microchamber devices matching the footprint of a standard 96-well plate were developed and used in conjunction with long-decay phosphorescent oxygen probes. These devices permit cell non-invasive, real-time monitoring of cellular respiration and a rapid, one-step, kinetic assessment of multiple samples for cell viability, drug/effector action. These assays can be carried out on conventional fluorescence plate readers, they are suitable for different types of cells, including adherent and slow-respiring cells, require small sample volumes and cell numbers, and are amenable for high throughput screening. Monitoring of as little as 300 mammalian cells in 3 microl volume has been demonstrated.

Biosensing Techniques↗

PubMed2003

RNA-related tools on the Bielefeld Bioinformatics Server.

We present four tools for the analysis of RNA secondary structure. They provide animated visualization of multiple structures, prediction of potential conformational switching, structure comparison (including local structure alignment) and prediction of structures potentially containing a certain kind of pseudoknots. All are available via the Bielefeld University Bioinformatics Server (http://bibiserv.techfak.uni-bielefeld.de).

Base Sequence↗

PubMed2003

Simulation-aided planning of quality-oriented personnel structures in production systems.

This paper presents research activities associated with the development of a simulation tool for modelling human reliability in production systems. This dynamic model enables the planner to determine the consequences of changes in human reliability on the quality of the production processes and the products. The model is built upon the basis of a tool for human reliability analysis ESAT (Experten-System zur Aufgaben-Taxonomie; Aufgabentaxonomie: Ein Verfahren zur Ermittlung der menschlichen Leistung bei der Durchführung von Aufgaben, Messerschmitt-Bölkow-Blohm, Ottobrunn, 1990.) and a personnel-oriented simulation programme ESPE (Engpassorientierte Simulation von Personalstrukturen; Ein engpassorientierter Ansatz zur simulationsunterstützten Planung von Personalstrukturen, Dissertation, Karlsruhe University, 1994), developed at the ifab-Institute of Human and Industrial Engineering at the University of Karlsruhe. In addition to the definition and the calculation of the human error probabilities, the consequences of the human errors (i.e. rework and waste) for the quality of the processes and the products were also implemented. This method is able to systematically plan quality-oriented assignments of personnel to functions and workplaces (personnel structures) in production systems. The effectiveness of the method is demonstrated by a case study.

Algorithms↗