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The Experts below are selected from a list of 99 Experts worldwide ranked by ideXlab platform

Bjoern Peters - One of the best experts on this subject based on the ideXlab platform.

  • TiArA: A Virtual Appliance for the Analysis of Tiling Array Data
    2013
    Co-Authors: Jason A. Greenbaum, Erika Assarsson, Jo L. Chung, Steven Head, Ro Sette, Bjoern Peters
    Abstract:

    Background: Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of userfriendly applications available for their analysis. Methodology/Principal Findings: Tiling Array Analyzer (TiArA) is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform. The background signal is empirically measured using a group of nonspecific probes with varying levels of GC content and normalization is performed to enforce a common dynamic range. Conclusions/Significance: TiArA is implemented as a standalone program for Linux systems and is available as a crossplatform virtual machine that will run under most modern operating systems using virtualization software such as Sun VirtualBox or VMware. The software is available as a Debian Package or a virtual appliance a

  • TiArA: a virtual appliance for the analysis of Tiling Array data.
    PloS one, 2010
    Co-Authors: Jason A. Greenbaum, Erika Assarsson, Jo L. Chung, Steven R. Head, Alessandro Sette, Bjoern Peters
    Abstract:

    Background Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of user-friendly applications available for their analysis. Methodology/Principal Findings Tiling Array Analyzer (TiArA) is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform. The background signal is empirically measured using a group of nonspecific probes with varying levels of GC content and normalization is performed to enforce a common dynamic range. Conclusions/Significance TiArA is implemented as a standalone program for Linux systems and is available as a cross-platform virtual machine that will run under most modern operating systems using virtualization software such as Sun VirtualBox or VMware. The software is available as a Debian Package or a virtual appliance at http://purl.org/NET/tiara.

  • TiArA: a virtual appliance for the analysis of Tiling Array data.
    Public Library of Science (PLoS), 2010
    Co-Authors: Jason A. Greenbaum, Erika Assarsson, Jo L. Chung, Alessandro Sette, Steven Head, Bjoern Peters
    Abstract:

    Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of user-friendly applications available for their analysis.Tiling Array Analyzer (TiArA) is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform. The background signal is empirically measured using a group of nonspecific probes with varying levels of GC content and normalization is performed to enforce a common dynamic range.TiArA is implemented as a standalone program for Linux systems and is available as a cross-platform virtual machine that will run under most modern operating systems using virtualization software such as Sun VirtualBox or VMware. The software is available as a Debian Package or a virtual appliance at http://purl.org/NET/tiara

Rudi Balling - One of the best experts on this subject based on the ideXlab platform.

  • MINERVA-a platform for visualization and curation of molecular interaction networks.
    NPJ systems biology and applications, 2016
    Co-Authors: Piotr Gawron, Fintan Mcgee, Venkata Satagopam, Alexander Mazein, Stephan Gebel, Benoit Otjacques, Simone Zorzan, Marek Ostaszewski, Michael Kuzma, Rudi Balling
    Abstract:

    Our growing knowledge about various molecular mechanisms is becoming increasingly more structured and accessible. Different repositories of molecular interactions and available literature enable construction of focused and high-quality molecular interaction networks. Novel tools for curation and exploration of such networks are needed, in order to foster the development of a systems biology environment. In particular, solutions for visualization, annotation and data cross-linking will facilitate usage of network-encoded knowledge in biomedical research. To this end we developed the MINERVA (Molecular Interaction NEtwoRks VisuAlization) platform, a standalone webservice supporting curation, annotation and visualization of molecular interaction networks in Systems Biology Graphical Notation (SBGN)-compliant format. MINERVA provides automated content annotation and verification for improved quality control. The end users can explore and interact with hosted networks, and provide direct feedback to content curators. MINERVA enables mapping drug targets or overlaying experimental data on the visualized networks. Extensive export functions enable downloading areas of the visualized networks as SBGN-compliant models for efficient reuse of hosted networks. The software is available under Affero GPL 3.0 as a Virtual Machine snapshot, Debian Package and Docker instance at http://r3lab.uni.lu/web/minerva-website/ . We believe that MINERVA is an important contribution to systems biology community, as its architecture enables set-up of locally or globally accessible SBGN-oriented repositories of molecular interaction networks. Its functionalities allow overlay of multiple information layers, facilitating exploration of content and interpretation of data. Moreover, annotation and verification workflows of MINERVA improve the efficiency of curation of networks, allowing life-science researchers to better engage in development and use of biomedical knowledge repositories. A web platform that integrates data on biological networks can help scientists obtain deeper insights into the inner workings of the cell. Life is powered by the complex interplay between myriad 'pathways' composed of interacting proteins, DNA and other biomolecules. Biologists have accumulated vast troves of data on these processes, and now researchers led by Piotr Gawron at the University of Luxembourg have built software that can combine these disparate datasets into a more meaningful 'big picture'. The Molecular Interaction Networks Visualization (MINERVA) platform allows users to interact directly with graphical representations of biological pathways as a means to understand the broader cellular impacts of both diseases and the drugs intended to treat them. The resulting maps can then be manually curated, annotated and exported to other bioinformatics platforms for use by the broader research community.

  • MINERVA—a platform for visualization and curation of molecular interaction networks
    npj Systems Biology and Applications, 2016
    Co-Authors: Piotr Gawroński, Mirjana Küzma, Fintan Mcgee, Venkata Satagopam, Alexander Mazein, Stephan Gebel, Benoit Otjacques, Simone Zorzan, Marek Ostaszewski, Rudi Balling
    Abstract:

    Our growing knowledge about various molecular mechanisms is becoming increasingly more structured and accessible. Different repositories of molecular interactions and available literature enable construction of focused and high-quality molecular interaction networks. Novel tools for curation and exploration of such networks are needed, in order to foster the development of a systems biology environment. In particular, solutions for visualization, annotation and data cross-linking will facilitate usage of network-encoded knowledge in biomedical research. To this end we developed the MINERVA (Molecular Interaction NEtwoRks VisuAlization) platform, a standalone webservice supporting curation, annotation and visualization of molecular interaction networks in Systems Biology Graphical Notation (SBGN)-compliant format. MINERVA provides automated content annotation and verification for improved quality control. The end users can explore and interact with hosted networks, and provide direct feedback to content curators. MINERVA enables mapping drug targets or overlaying experimental data on the visualized networks. Extensive export functions enable downloading areas of the visualized networks as SBGN-compliant models for efficient reuse of hosted networks. The software is available under Affero GPL 3.0 as a Virtual Machine snapshot, Debian Package and Docker instance at http://r3lab. uni.lu/web/minerva-website/. We believe that MINERVA is an important contribution to systems biology community, as its architecture enables set-up of locally or globally accessible SBGN-oriented repositories of molecular interaction networks. Its functionalities allow overlay of multiple information layers, facilitating exploration of content and interpretation of data. Moreover, annotation and verification workflows of MINERVA improve the efficiency of curation of networks, allowing life-science researchers to better engage in development and use of biomedical knowledge repositories.

Jason A. Greenbaum - One of the best experts on this subject based on the ideXlab platform.

  • TiArA: A Virtual Appliance for the Analysis of Tiling Array Data
    2013
    Co-Authors: Jason A. Greenbaum, Erika Assarsson, Jo L. Chung, Steven Head, Ro Sette, Bjoern Peters
    Abstract:

    Background: Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of userfriendly applications available for their analysis. Methodology/Principal Findings: Tiling Array Analyzer (TiArA) is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform. The background signal is empirically measured using a group of nonspecific probes with varying levels of GC content and normalization is performed to enforce a common dynamic range. Conclusions/Significance: TiArA is implemented as a standalone program for Linux systems and is available as a crossplatform virtual machine that will run under most modern operating systems using virtualization software such as Sun VirtualBox or VMware. The software is available as a Debian Package or a virtual appliance a

  • TiArA: a virtual appliance for the analysis of Tiling Array data.
    PloS one, 2010
    Co-Authors: Jason A. Greenbaum, Erika Assarsson, Jo L. Chung, Steven R. Head, Alessandro Sette, Bjoern Peters
    Abstract:

    Background Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of user-friendly applications available for their analysis. Methodology/Principal Findings Tiling Array Analyzer (TiArA) is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform. The background signal is empirically measured using a group of nonspecific probes with varying levels of GC content and normalization is performed to enforce a common dynamic range. Conclusions/Significance TiArA is implemented as a standalone program for Linux systems and is available as a cross-platform virtual machine that will run under most modern operating systems using virtualization software such as Sun VirtualBox or VMware. The software is available as a Debian Package or a virtual appliance at http://purl.org/NET/tiara.

  • TiArA: a virtual appliance for the analysis of Tiling Array data.
    Public Library of Science (PLoS), 2010
    Co-Authors: Jason A. Greenbaum, Erika Assarsson, Jo L. Chung, Alessandro Sette, Steven Head, Bjoern Peters
    Abstract:

    Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of user-friendly applications available for their analysis.Tiling Array Analyzer (TiArA) is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform. The background signal is empirically measured using a group of nonspecific probes with varying levels of GC content and normalization is performed to enforce a common dynamic range.TiArA is implemented as a standalone program for Linux systems and is available as a cross-platform virtual machine that will run under most modern operating systems using virtualization software such as Sun VirtualBox or VMware. The software is available as a Debian Package or a virtual appliance at http://purl.org/NET/tiara

Jo L. Chung - One of the best experts on this subject based on the ideXlab platform.

  • TiArA: A Virtual Appliance for the Analysis of Tiling Array Data
    2013
    Co-Authors: Jason A. Greenbaum, Erika Assarsson, Jo L. Chung, Steven Head, Ro Sette, Bjoern Peters
    Abstract:

    Background: Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of userfriendly applications available for their analysis. Methodology/Principal Findings: Tiling Array Analyzer (TiArA) is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform. The background signal is empirically measured using a group of nonspecific probes with varying levels of GC content and normalization is performed to enforce a common dynamic range. Conclusions/Significance: TiArA is implemented as a standalone program for Linux systems and is available as a crossplatform virtual machine that will run under most modern operating systems using virtualization software such as Sun VirtualBox or VMware. The software is available as a Debian Package or a virtual appliance a

  • TiArA: a virtual appliance for the analysis of Tiling Array data.
    PloS one, 2010
    Co-Authors: Jason A. Greenbaum, Erika Assarsson, Jo L. Chung, Steven R. Head, Alessandro Sette, Bjoern Peters
    Abstract:

    Background Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of user-friendly applications available for their analysis. Methodology/Principal Findings Tiling Array Analyzer (TiArA) is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform. The background signal is empirically measured using a group of nonspecific probes with varying levels of GC content and normalization is performed to enforce a common dynamic range. Conclusions/Significance TiArA is implemented as a standalone program for Linux systems and is available as a cross-platform virtual machine that will run under most modern operating systems using virtualization software such as Sun VirtualBox or VMware. The software is available as a Debian Package or a virtual appliance at http://purl.org/NET/tiara.

  • TiArA: a virtual appliance for the analysis of Tiling Array data.
    Public Library of Science (PLoS), 2010
    Co-Authors: Jason A. Greenbaum, Erika Assarsson, Jo L. Chung, Alessandro Sette, Steven Head, Bjoern Peters
    Abstract:

    Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of user-friendly applications available for their analysis.Tiling Array Analyzer (TiArA) is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform. The background signal is empirically measured using a group of nonspecific probes with varying levels of GC content and normalization is performed to enforce a common dynamic range.TiArA is implemented as a standalone program for Linux systems and is available as a cross-platform virtual machine that will run under most modern operating systems using virtualization software such as Sun VirtualBox or VMware. The software is available as a Debian Package or a virtual appliance at http://purl.org/NET/tiara

Erika Assarsson - One of the best experts on this subject based on the ideXlab platform.

  • TiArA: A Virtual Appliance for the Analysis of Tiling Array Data
    2013
    Co-Authors: Jason A. Greenbaum, Erika Assarsson, Jo L. Chung, Steven Head, Ro Sette, Bjoern Peters
    Abstract:

    Background: Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of userfriendly applications available for their analysis. Methodology/Principal Findings: Tiling Array Analyzer (TiArA) is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform. The background signal is empirically measured using a group of nonspecific probes with varying levels of GC content and normalization is performed to enforce a common dynamic range. Conclusions/Significance: TiArA is implemented as a standalone program for Linux systems and is available as a crossplatform virtual machine that will run under most modern operating systems using virtualization software such as Sun VirtualBox or VMware. The software is available as a Debian Package or a virtual appliance a

  • TiArA: a virtual appliance for the analysis of Tiling Array data.
    PloS one, 2010
    Co-Authors: Jason A. Greenbaum, Erika Assarsson, Jo L. Chung, Steven R. Head, Alessandro Sette, Bjoern Peters
    Abstract:

    Background Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of user-friendly applications available for their analysis. Methodology/Principal Findings Tiling Array Analyzer (TiArA) is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform. The background signal is empirically measured using a group of nonspecific probes with varying levels of GC content and normalization is performed to enforce a common dynamic range. Conclusions/Significance TiArA is implemented as a standalone program for Linux systems and is available as a cross-platform virtual machine that will run under most modern operating systems using virtualization software such as Sun VirtualBox or VMware. The software is available as a Debian Package or a virtual appliance at http://purl.org/NET/tiara.

  • TiArA: a virtual appliance for the analysis of Tiling Array data.
    Public Library of Science (PLoS), 2010
    Co-Authors: Jason A. Greenbaum, Erika Assarsson, Jo L. Chung, Alessandro Sette, Steven Head, Bjoern Peters
    Abstract:

    Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of user-friendly applications available for their analysis.Tiling Array Analyzer (TiArA) is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform. The background signal is empirically measured using a group of nonspecific probes with varying levels of GC content and normalization is performed to enforce a common dynamic range.TiArA is implemented as a standalone program for Linux systems and is available as a cross-platform virtual machine that will run under most modern operating systems using virtualization software such as Sun VirtualBox or VMware. The software is available as a Debian Package or a virtual appliance at http://purl.org/NET/tiara

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