The Experts below are selected from a list of 285 Experts worldwide ranked by ideXlab platform

Elisabeth Rossmanith - One of the best experts on this subject based on the ideXlab platform.

Jeanfrancois Martin - One of the best experts on this subject based on the ideXlab platform.

  • qdd Version 3 1 a user friendly computer program for microsatellite selection and primer design revisited experimental validation of variables determining genotyping success rate
    Molecular Ecology Resources, 2014
    Co-Authors: Emese Meglecz, Nicolas Pech, Pascal Hingamp, Aurelie Trilles, Remi Grenier, Vincent Dubut, André Gilles, Jeanfrancois Martin
    Abstract:

    Microsatellite marker development has been greatly simplified by the use of high-throughput sequencing followed by in silico microsatellite detection and primer design. However, the selection of markers designed by the existing pipeLines depends either on arbitrary criteria, or older studies on PCR success. Based on wet laboratory experiments, we have identified the following factors that are most likely to influence genotyping success rate: alignment score between the primers and the amplicon; the distance between primers and microsatellites; the length of the PCR product; target region complexity and the number of reads underlying the sequence. The QDD pipeLine has been modified to include these most pertinent factors in the output to help the selection of markers. Furthermore, new features are also included in the present Version: (i) not only raw sequencing reads are accepted as input, but also contigs, allowing the analysis of assembled high-coverage data; (ii) input data can be both in fasta and fastq format to facilitate the use of Illumina and IonTorrent reads; (iii) A comparison to known transposable elements allows their detection; (iv) A contamination check can be carried out by BLASTing potential markers against the nucleotide (nt) database of NCBI; (v) QDD3 is now also available imbedded into a virtual machine making installation easier and operating system independent. It can be used both on Command-Line Version as well as integrated into a Galaxy server, providing a user-friendly interface, as well as the possibility to utilize a large variety of NGS tools.

  • QDD Version 3.1: a user‐friendly computer program for microsatellite selection and primer design revisited: experimental validation of variables determining genotyping success rate
    Molecular Ecology Resources, 2014
    Co-Authors: Emese Meglecz, Nicolas Pech, Pascal Hingamp, Aurelie Trilles, Remi Grenier, Vincent Dubut, André Gilles, Jeanfrancois Martin
    Abstract:

    : Microsatellite marker development has been greatly simplified by the use of high-throughput sequencing followed by in silico microsatellite detection and primer design. However, the selection of markers designed by the existing pipeLines depends either on arbitrary criteria, or older studies on PCR success. Based on wet laboratory experiments, we have identified the following factors that are most likely to influence genotyping success rate: alignment score between the primers and the amplicon; the distance between primers and microsatellites; the length of the PCR product; target region complexity and the number of reads underlying the sequence. The QDD pipeLine has been modified to include these most pertinent factors in the output to help the selection of markers. Furthermore, new features are also included in the present Version: (i) not only raw sequencing reads are accepted as input, but also contigs, allowing the analysis of assembled high-coverage data; (ii) input data can be both in fasta and fastq format to facilitate the use of Illumina and IonTorrent reads; (iii) A comparison to known transposable elements allows their detection; (iv) A contamination check can be carried out by BLASTing potential markers against the nucleotide (nt) database of NCBI; (v) QDD3 is now also available imbedded into a virtual machine making installation easier and operating system independent. It can be used both on Command-Line Version as well as integrated into a Galaxy server, providing a user-friendly interface, as well as the possibility to utilize a large variety of NGS tools.

Peter Kemper - One of the best experts on this subject based on the ideXlab platform.

  • DSN - Report generation for simulation traces with Traviando
    2009 IEEE IFIP International Conference on Dependable Systems & Networks, 2009
    Co-Authors: Peter Kemper
    Abstract:

    Any model-based evaluation of the dependability of a system requires validation and verification to justify that its results are meaningful. Modern modeling frameworks enable us to create and evaluate models of great complexity. However, we believe that much more can be done to support a modeler in ensuring that the dynamic behavior of an executable simulation model is consistent with the modeler's understanding. In this paper, we describe a new Command Line Version of Traviando that reads an execution trace of a discrete event simulation and generates a set of HTML formatted web pages to document properties that it recognizes from its input. Those properties include characteristics of state variables as well as changes to state variables that are performed by events. The point is to highlight the content of a simulation run in a format that is immediately accessible and understandable.

  • QEST - Recent Extensions to Traviando
    2009 Sixth International Conference on the Quantitative Evaluation of Systems, 2009
    Co-Authors: Peter Kemper
    Abstract:

    Traviando is a trace analyzer and visualizer for simulation traces of discrete event dynamic systems. In this paper, we briefly outLine recent extensions of Traviando towards an identification of model invariants and a detection of partial deadlocks and immediate events. This new functionality complements an existing model-checker and event browser. In addition to the graphical user interface, a new Command-Line Version of the tool allows a user to obtain analysis results being documented in a set of generated web pages, which minimizes the learning curve for the use of Traviando to obtain some feedback on the details of a simulation run.

  • Recent Extensions to Traviando
    2009 Sixth International Conference on the Quantitative Evaluation of Systems, 2009
    Co-Authors: Peter Kemper
    Abstract:

    Traviando is a trace analyzer and visualizer for simulation traces of discrete event dynamic systems. In this paper, we briefly outLine recent extensions of Traviando towards an identification of model invariants and a detection of partial deadlocks and immediate events. This new functionality complements an existing model-checker and event browser. In addition to the graphical user interface, a new Command-Line Version of the tool allows a user to obtain analysis results being documented in a set of generated Web pages, which minimizes the learning curve for the use of Traviando to obtain some feedback on the details of a simulation run.

  • Report generation for simulation traces with Traviando
    2009 IEEE IFIP International Conference on Dependable Systems & Networks, 2009
    Co-Authors: Peter Kemper
    Abstract:

    Any model-based evaluation of the dependability of a system requires validation and verification to justify that its results are meaningful. Modern modeling frameworks enable us to create and evaluate models of great complexity. However, we believe that much more can be done to support a modeler in ensuring that the dynamic behavior of an executable simulation model is consistent with the modeler's understanding. In this paper, we describe a new Command Line Version of Traviando that reads an execution trace of a discrete event simulation and generates a set of HTML formatted Web pages to document properties that it recognizes from its input. Those properties include characteristics of state variables as well as changes to state variables that are performed by events. The point is to highlight the content of a simulation run in a format that is immediately accessible and understandable.

Emese Meglecz - One of the best experts on this subject based on the ideXlab platform.

  • qdd Version 3 1 a user friendly computer program for microsatellite selection and primer design revisited experimental validation of variables determining genotyping success rate
    Molecular Ecology Resources, 2014
    Co-Authors: Emese Meglecz, Nicolas Pech, Pascal Hingamp, Aurelie Trilles, Remi Grenier, Vincent Dubut, André Gilles, Jeanfrancois Martin
    Abstract:

    Microsatellite marker development has been greatly simplified by the use of high-throughput sequencing followed by in silico microsatellite detection and primer design. However, the selection of markers designed by the existing pipeLines depends either on arbitrary criteria, or older studies on PCR success. Based on wet laboratory experiments, we have identified the following factors that are most likely to influence genotyping success rate: alignment score between the primers and the amplicon; the distance between primers and microsatellites; the length of the PCR product; target region complexity and the number of reads underlying the sequence. The QDD pipeLine has been modified to include these most pertinent factors in the output to help the selection of markers. Furthermore, new features are also included in the present Version: (i) not only raw sequencing reads are accepted as input, but also contigs, allowing the analysis of assembled high-coverage data; (ii) input data can be both in fasta and fastq format to facilitate the use of Illumina and IonTorrent reads; (iii) A comparison to known transposable elements allows their detection; (iv) A contamination check can be carried out by BLASTing potential markers against the nucleotide (nt) database of NCBI; (v) QDD3 is now also available imbedded into a virtual machine making installation easier and operating system independent. It can be used both on Command-Line Version as well as integrated into a Galaxy server, providing a user-friendly interface, as well as the possibility to utilize a large variety of NGS tools.

  • QDD Version 3.1: a user‐friendly computer program for microsatellite selection and primer design revisited: experimental validation of variables determining genotyping success rate
    Molecular Ecology Resources, 2014
    Co-Authors: Emese Meglecz, Nicolas Pech, Pascal Hingamp, Aurelie Trilles, Remi Grenier, Vincent Dubut, André Gilles, Jeanfrancois Martin
    Abstract:

    : Microsatellite marker development has been greatly simplified by the use of high-throughput sequencing followed by in silico microsatellite detection and primer design. However, the selection of markers designed by the existing pipeLines depends either on arbitrary criteria, or older studies on PCR success. Based on wet laboratory experiments, we have identified the following factors that are most likely to influence genotyping success rate: alignment score between the primers and the amplicon; the distance between primers and microsatellites; the length of the PCR product; target region complexity and the number of reads underlying the sequence. The QDD pipeLine has been modified to include these most pertinent factors in the output to help the selection of markers. Furthermore, new features are also included in the present Version: (i) not only raw sequencing reads are accepted as input, but also contigs, allowing the analysis of assembled high-coverage data; (ii) input data can be both in fasta and fastq format to facilitate the use of Illumina and IonTorrent reads; (iii) A comparison to known transposable elements allows their detection; (iv) A contamination check can be carried out by BLASTing potential markers against the nucleotide (nt) database of NCBI; (v) QDD3 is now also available imbedded into a virtual machine making installation easier and operating system independent. It can be used both on Command-Line Version as well as integrated into a Galaxy server, providing a user-friendly interface, as well as the possibility to utilize a large variety of NGS tools.

Fuli Yu - One of the best experts on this subject based on the ideXlab platform.

  • An integrative variant analysis suite for whole exome next-generation sequencing data
    BMC Bioinformatics, 2012
    Co-Authors: Danny Challis, Jin Yu, Uday S Evani, Andrew R Jackson, Sameer Paithankar, Cristian Coarfa, Aleksandar Milosavljevic, Richard A Gibbs, Fuli Yu
    Abstract:

    Background Whole exome capture sequencing allows researchers to cost-effectively sequence the coding regions of the genome. Although the exome capture sequencing methods have become routine and well established, there is currently a lack of tools specialized for variant calling in this type of data. Results Using statistical models trained on validated whole-exome capture sequencing data, the Atlas2 Suite is an integrative variant analysis pipeLine optimized for variant discovery on all three of the widely used next generation sequencing platforms (SOLiD, Illumina, and Roche 454). The suite employs logistic regression models in conjunction with user-adjustable cutoffs to accurately separate true SNPs and INDELs from sequencing and mapping errors with high sensitivity (96.7%). Conclusion We have implemented the Atlas2 Suite and applied it to 92 whole exome samples from the 1000 Genomes Project. The Atlas2 Suite is available for download at http://sourceforge.net/projects/atlas2/ . In addition to a Command Line Version, the suite has been integrated into the Genboree Workbench, allowing biomedical scientists with minimal informatics expertise to remotely call, view, and further analyze variants through a simple web interface. The existing genomic databases displayed via the Genboree browser also streamLine the process from variant discovery to functional genomics analysis, resulting in an off-the-shelf toolkit for the broader community.