Simulation Experiment

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Frank Bergmann - One of the best experts on this subject based on the ideXlab platform.

  • Simulation Experiment description markup language sed ml level 1 version 3 l1v3
    Journal of Integrative Bioinformatics, 2015
    Co-Authors: Frank Bergmann, Jonathan Cooper, Matthias Konig, Ion I Moraru, David Nickerson, Nicolas Le Novere, Brett G Olivier
    Abstract:

    The creation of computational Simulation Experiments to inform modern biological research poses challenges to reproduce, annotate, archive, and share such Experiments. Efforts such as SBML or CellML standardize the formal representation of computational models in various areas of biology. The Simulation Experiment Description Markup Language (SED-ML) describes what procedures the models are subjected to, and the details of those procedures. These standards, together with further COMBINE standards, describe models sufficiently well for the reproduction of Simulation studies among users and software tools. The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format that encodes, for a given Simulation Experiment, (i) which models to use; (ii) which modifications to apply to models before Simulation; (iii) which Simulation procedures to run on each model; (iv) how to post-process the data; and (v) how these results should be plotted and reported. SED-ML Level 1 Version 1 (L1V1) implemented support for the encoding of basic time course Simulations. SED-ML L1V2 added support for more complex types of Simulations, specifically repeated tasks and chained Simulation procedures. SED-ML L1V3 extends L1V2 by means to describe which datasets and subsets thereof to use within a Simulation Experiment.

  • reproducible computational biology Experiments with sed ml the Simulation Experiment description markup language
    BMC Systems Biology, 2011
    Co-Authors: Dagmar Waltemath, Richard R Adams, Frank Bergmann, Ion I Moraru, Michael Hucka, Fedor A Kolpakov, Andrew K Miller, David P Nickerson, Sven Sahle, Jacky L Snoep
    Abstract:

    The increasing use of computational Simulation Experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such Experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of Simulation Experiments among users and software tools. In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of Simulation Experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of Simulation Experiments in the area, namely time course Simulations. SED-ML documents specify which models to use in an Experiment, modifications to apply on the models before using them, which Simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of Simulation Experiments; it is not specific to particular Simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable Simulation descriptions. With SED-ML, software can exchange Simulation Experiment descriptions, enabling the validation and reuse of Simulation Experiments in different tools. Authors of papers reporting Simulation Experiments can make their Simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, Experiments covering models from different fields of research can be accurately described and combined.

  • reproducible computational biology Experiments with sed ml the Simulation Experiment description markup language
    BMC Systems Biology, 2011
    Co-Authors: Dagmar Waltemath, Richard R Adams, Frank Bergmann, Ion I Moraru, David Nickerson, Michael Hucka, Fedor A Kolpakov, Andrew K Miller, Sven Sahle, Jacky L Snoep
    Abstract:

    Background The increasing use of computational Simulation Experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such Experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of Simulation Experiments among users and software tools.

  • minimum information about a Simulation Experiment miase
    PLOS Computational Biology, 2011
    Co-Authors: Dagmar Waltemath, Richard R Adams, Daniel A Beard, Frank Bergmann, Upinder S Bhalla, Randall Britten, Vijayalakshmi Chelliah, M T Cooling, Jonathan Cooper
    Abstract:

    Reproducibility of Experiments is a basic requirement for science. Minimum Information (MI) guidelines have proved a helpful means of enabling reuse of existing work in modern biology. The Minimum Information Required in the Annotation of Models (MIRIAM) guidelines promote the exchange and reuse of biochemical computational models. However, information about a model alone is not sufficient to enable its efficient reuse in a computational setting. Advanced numerical algorithms and complex modeling workflows used in modern computational biology make reproduction of Simulations difficult. It is therefore essential to define the core information necessary to perform Simulations of those models. The Minimum Information About a Simulation Experiment (MIASE, Glossary in Box 1) describes the minimal set of information that must be provided to make the description of a Simulation Experiment available to others. It includes the list of models to use and their modifications, all the Simulation procedures to apply and in which order, the processing of the raw numerical results, and the description of the final output. MIASE allows for the reproduction of any Simulation Experiment. The provision of this information, along with a set of required models, guarantees that the Simulation Experiment represents the intention of the original authors. Following MIASE guidelines will thus improve the quality of scientific reporting, and will also allow collaborative, more distributed efforts in computational modeling and Simulation of biological processes.

  • Simulation Experiment description markup language sed ml level 1 version 1
    Nature Precedings, 2011
    Co-Authors: Dagmar Waltemath, Richard R Adams, Frank Bergmann, Nicolas Le Novere
    Abstract:

    The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for encoding Simulation Experiments, following the requirements defined in the MIASE guidelines. SED-ML allows one to define the model to use, the Experimental task to run, and which result to produce.

Dagmar Waltemath - One of the best experts on this subject based on the ideXlab platform.

  • reproducible computational biology Experiments with sed ml the Simulation Experiment description markup language
    BMC Systems Biology, 2011
    Co-Authors: Dagmar Waltemath, Richard R Adams, Frank Bergmann, Ion I Moraru, Michael Hucka, Fedor A Kolpakov, Andrew K Miller, David P Nickerson, Sven Sahle, Jacky L Snoep
    Abstract:

    The increasing use of computational Simulation Experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such Experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of Simulation Experiments among users and software tools. In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of Simulation Experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of Simulation Experiments in the area, namely time course Simulations. SED-ML documents specify which models to use in an Experiment, modifications to apply on the models before using them, which Simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of Simulation Experiments; it is not specific to particular Simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable Simulation descriptions. With SED-ML, software can exchange Simulation Experiment descriptions, enabling the validation and reuse of Simulation Experiments in different tools. Authors of papers reporting Simulation Experiments can make their Simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, Experiments covering models from different fields of research can be accurately described and combined.

  • reproducible computational biology Experiments with sed ml the Simulation Experiment description markup language
    BMC Systems Biology, 2011
    Co-Authors: Dagmar Waltemath, Richard R Adams, Frank Bergmann, Ion I Moraru, David Nickerson, Michael Hucka, Fedor A Kolpakov, Andrew K Miller, Sven Sahle, Jacky L Snoep
    Abstract:

    Background The increasing use of computational Simulation Experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such Experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of Simulation Experiments among users and software tools.

  • minimum information about a Simulation Experiment miase
    PLOS Computational Biology, 2011
    Co-Authors: Dagmar Waltemath, Richard R Adams, Daniel A Beard, Frank Bergmann, Upinder S Bhalla, Randall Britten, Vijayalakshmi Chelliah, M T Cooling, Jonathan Cooper
    Abstract:

    Reproducibility of Experiments is a basic requirement for science. Minimum Information (MI) guidelines have proved a helpful means of enabling reuse of existing work in modern biology. The Minimum Information Required in the Annotation of Models (MIRIAM) guidelines promote the exchange and reuse of biochemical computational models. However, information about a model alone is not sufficient to enable its efficient reuse in a computational setting. Advanced numerical algorithms and complex modeling workflows used in modern computational biology make reproduction of Simulations difficult. It is therefore essential to define the core information necessary to perform Simulations of those models. The Minimum Information About a Simulation Experiment (MIASE, Glossary in Box 1) describes the minimal set of information that must be provided to make the description of a Simulation Experiment available to others. It includes the list of models to use and their modifications, all the Simulation procedures to apply and in which order, the processing of the raw numerical results, and the description of the final output. MIASE allows for the reproduction of any Simulation Experiment. The provision of this information, along with a set of required models, guarantees that the Simulation Experiment represents the intention of the original authors. Following MIASE guidelines will thus improve the quality of scientific reporting, and will also allow collaborative, more distributed efforts in computational modeling and Simulation of biological processes.

  • Simulation Experiment description markup language sed ml level 1 version 1
    Nature Precedings, 2011
    Co-Authors: Dagmar Waltemath, Richard R Adams, Frank Bergmann, Nicolas Le Novere
    Abstract:

    The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for encoding Simulation Experiments, following the requirements defined in the MIASE guidelines. SED-ML allows one to define the model to use, the Experimental task to run, and which result to produce.

Jacky L Snoep - One of the best experts on this subject based on the ideXlab platform.

  • reproducible computational biology Experiments with sed ml the Simulation Experiment description markup language
    BMC Systems Biology, 2011
    Co-Authors: Dagmar Waltemath, Richard R Adams, Frank Bergmann, Ion I Moraru, Michael Hucka, Fedor A Kolpakov, Andrew K Miller, David P Nickerson, Sven Sahle, Jacky L Snoep
    Abstract:

    The increasing use of computational Simulation Experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such Experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of Simulation Experiments among users and software tools. In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of Simulation Experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of Simulation Experiments in the area, namely time course Simulations. SED-ML documents specify which models to use in an Experiment, modifications to apply on the models before using them, which Simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of Simulation Experiments; it is not specific to particular Simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable Simulation descriptions. With SED-ML, software can exchange Simulation Experiment descriptions, enabling the validation and reuse of Simulation Experiments in different tools. Authors of papers reporting Simulation Experiments can make their Simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, Experiments covering models from different fields of research can be accurately described and combined.

  • reproducible computational biology Experiments with sed ml the Simulation Experiment description markup language
    BMC Systems Biology, 2011
    Co-Authors: Dagmar Waltemath, Richard R Adams, Frank Bergmann, Ion I Moraru, David Nickerson, Michael Hucka, Fedor A Kolpakov, Andrew K Miller, Sven Sahle, Jacky L Snoep
    Abstract:

    Background The increasing use of computational Simulation Experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such Experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of Simulation Experiments among users and software tools.

Richard R Adams - One of the best experts on this subject based on the ideXlab platform.

  • reproducible computational biology Experiments with sed ml the Simulation Experiment description markup language
    BMC Systems Biology, 2011
    Co-Authors: Dagmar Waltemath, Richard R Adams, Frank Bergmann, Ion I Moraru, Michael Hucka, Fedor A Kolpakov, Andrew K Miller, David P Nickerson, Sven Sahle, Jacky L Snoep
    Abstract:

    The increasing use of computational Simulation Experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such Experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of Simulation Experiments among users and software tools. In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of Simulation Experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of Simulation Experiments in the area, namely time course Simulations. SED-ML documents specify which models to use in an Experiment, modifications to apply on the models before using them, which Simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of Simulation Experiments; it is not specific to particular Simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable Simulation descriptions. With SED-ML, software can exchange Simulation Experiment descriptions, enabling the validation and reuse of Simulation Experiments in different tools. Authors of papers reporting Simulation Experiments can make their Simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, Experiments covering models from different fields of research can be accurately described and combined.

  • reproducible computational biology Experiments with sed ml the Simulation Experiment description markup language
    BMC Systems Biology, 2011
    Co-Authors: Dagmar Waltemath, Richard R Adams, Frank Bergmann, Ion I Moraru, David Nickerson, Michael Hucka, Fedor A Kolpakov, Andrew K Miller, Sven Sahle, Jacky L Snoep
    Abstract:

    Background The increasing use of computational Simulation Experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such Experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of Simulation Experiments among users and software tools.

  • minimum information about a Simulation Experiment miase
    PLOS Computational Biology, 2011
    Co-Authors: Dagmar Waltemath, Richard R Adams, Daniel A Beard, Frank Bergmann, Upinder S Bhalla, Randall Britten, Vijayalakshmi Chelliah, M T Cooling, Jonathan Cooper
    Abstract:

    Reproducibility of Experiments is a basic requirement for science. Minimum Information (MI) guidelines have proved a helpful means of enabling reuse of existing work in modern biology. The Minimum Information Required in the Annotation of Models (MIRIAM) guidelines promote the exchange and reuse of biochemical computational models. However, information about a model alone is not sufficient to enable its efficient reuse in a computational setting. Advanced numerical algorithms and complex modeling workflows used in modern computational biology make reproduction of Simulations difficult. It is therefore essential to define the core information necessary to perform Simulations of those models. The Minimum Information About a Simulation Experiment (MIASE, Glossary in Box 1) describes the minimal set of information that must be provided to make the description of a Simulation Experiment available to others. It includes the list of models to use and their modifications, all the Simulation procedures to apply and in which order, the processing of the raw numerical results, and the description of the final output. MIASE allows for the reproduction of any Simulation Experiment. The provision of this information, along with a set of required models, guarantees that the Simulation Experiment represents the intention of the original authors. Following MIASE guidelines will thus improve the quality of scientific reporting, and will also allow collaborative, more distributed efforts in computational modeling and Simulation of biological processes.

  • Simulation Experiment description markup language sed ml level 1 version 1
    Nature Precedings, 2011
    Co-Authors: Dagmar Waltemath, Richard R Adams, Frank Bergmann, Nicolas Le Novere
    Abstract:

    The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for encoding Simulation Experiments, following the requirements defined in the MIASE guidelines. SED-ML allows one to define the model to use, the Experimental task to run, and which result to produce.

Ion I Moraru - One of the best experts on this subject based on the ideXlab platform.

  • Simulation Experiment description markup language sed ml level 1 version 3 l1v3
    Journal of Integrative Bioinformatics, 2015
    Co-Authors: Frank Bergmann, Jonathan Cooper, Matthias Konig, Ion I Moraru, David Nickerson, Nicolas Le Novere, Brett G Olivier
    Abstract:

    The creation of computational Simulation Experiments to inform modern biological research poses challenges to reproduce, annotate, archive, and share such Experiments. Efforts such as SBML or CellML standardize the formal representation of computational models in various areas of biology. The Simulation Experiment Description Markup Language (SED-ML) describes what procedures the models are subjected to, and the details of those procedures. These standards, together with further COMBINE standards, describe models sufficiently well for the reproduction of Simulation studies among users and software tools. The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format that encodes, for a given Simulation Experiment, (i) which models to use; (ii) which modifications to apply to models before Simulation; (iii) which Simulation procedures to run on each model; (iv) how to post-process the data; and (v) how these results should be plotted and reported. SED-ML Level 1 Version 1 (L1V1) implemented support for the encoding of basic time course Simulations. SED-ML L1V2 added support for more complex types of Simulations, specifically repeated tasks and chained Simulation procedures. SED-ML L1V3 extends L1V2 by means to describe which datasets and subsets thereof to use within a Simulation Experiment.

  • reproducible computational biology Experiments with sed ml the Simulation Experiment description markup language
    BMC Systems Biology, 2011
    Co-Authors: Dagmar Waltemath, Richard R Adams, Frank Bergmann, Ion I Moraru, Michael Hucka, Fedor A Kolpakov, Andrew K Miller, David P Nickerson, Sven Sahle, Jacky L Snoep
    Abstract:

    The increasing use of computational Simulation Experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such Experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of Simulation Experiments among users and software tools. In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of Simulation Experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of Simulation Experiments in the area, namely time course Simulations. SED-ML documents specify which models to use in an Experiment, modifications to apply on the models before using them, which Simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of Simulation Experiments; it is not specific to particular Simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable Simulation descriptions. With SED-ML, software can exchange Simulation Experiment descriptions, enabling the validation and reuse of Simulation Experiments in different tools. Authors of papers reporting Simulation Experiments can make their Simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, Experiments covering models from different fields of research can be accurately described and combined.

  • reproducible computational biology Experiments with sed ml the Simulation Experiment description markup language
    BMC Systems Biology, 2011
    Co-Authors: Dagmar Waltemath, Richard R Adams, Frank Bergmann, Ion I Moraru, David Nickerson, Michael Hucka, Fedor A Kolpakov, Andrew K Miller, Sven Sahle, Jacky L Snoep
    Abstract:

    Background The increasing use of computational Simulation Experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such Experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of Simulation Experiments among users and software tools.