The Experts below are selected from a list of 111 Experts worldwide ranked by ideXlab platform

Antoniotti Marco - One of the best experts on this subject based on the ideXlab platform.

  • SBML Level : an extensible format for the 3 exchange and Reuse of biological Models
    'EMBO', 2020
    Co-Authors: Keating Sarah, Bergmann Frank, Helikar Tomáš, Malik‐sheriff Rahuman, Moraru Ion, Meier‐schellersheim Martin, Adams Richard, Allen Nicholas, Angermann Bastian, Antoniotti Marco
    Abstract:

    International audienceSystems biology has experienced dramatic growth in the number, size, and complexity of computational Models. To reproduce simulation results and Reuse Models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based Models and packages that extend the core with features suited to other model types including constraint-based Models, reaction-diffusion Models, logical network Models, and rule-based Models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with Models. More recently, the rise of multi-scale Models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with Models. We provide our perspectives on the challenges presented by these developments and how SBML Level provides the foundation needed to support this evolution.

Marco Antoniotti - One of the best experts on this subject based on the ideXlab platform.

  • SBML Level : an extensible format for the 3 exchange and Reuse of biological Models
    Molecular Systems Biology, 2020
    Co-Authors: Sarah Keating, Frank Bergmann, Tomáš Helikar, Rahuman Malik‐sheriff, Ion Moraru, Martin Meier‐schellersheim, Richard Adams, Nicholas Allen, Bastian Angermann, Marco Antoniotti
    Abstract:

    Systems biology has experienced dramatic growth in the number, size, and complexity of computational Models. To reproduce simulation results and Reuse Models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based Models and packages that extend the core with features suited to other model types including constraint-based Models, reaction-diffusion Models, logical network Models, and rule-based Models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with Models. More recently, the rise of multi-scale Models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with Models. We provide our perspectives on the challenges presented by these developments and how SBML Level provides the foundation needed to support this evolution. 3

Keating Sarah - One of the best experts on this subject based on the ideXlab platform.

  • SBML Level : an extensible format for the 3 exchange and Reuse of biological Models
    'EMBO', 2020
    Co-Authors: Keating Sarah, Bergmann Frank, Helikar Tomáš, Malik‐sheriff Rahuman, Moraru Ion, Meier‐schellersheim Martin, Adams Richard, Allen Nicholas, Angermann Bastian, Antoniotti Marco
    Abstract:

    International audienceSystems biology has experienced dramatic growth in the number, size, and complexity of computational Models. To reproduce simulation results and Reuse Models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based Models and packages that extend the core with features suited to other model types including constraint-based Models, reaction-diffusion Models, logical network Models, and rule-based Models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with Models. More recently, the rise of multi-scale Models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with Models. We provide our perspectives on the challenges presented by these developments and how SBML Level provides the foundation needed to support this evolution.

Sarah Keating - One of the best experts on this subject based on the ideXlab platform.

  • SBML Level : an extensible format for the 3 exchange and Reuse of biological Models
    Molecular Systems Biology, 2020
    Co-Authors: Sarah Keating, Frank Bergmann, Tomáš Helikar, Rahuman Malik‐sheriff, Ion Moraru, Martin Meier‐schellersheim, Richard Adams, Nicholas Allen, Bastian Angermann, Marco Antoniotti
    Abstract:

    Systems biology has experienced dramatic growth in the number, size, and complexity of computational Models. To reproduce simulation results and Reuse Models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based Models and packages that extend the core with features suited to other model types including constraint-based Models, reaction-diffusion Models, logical network Models, and rule-based Models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with Models. More recently, the rise of multi-scale Models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with Models. We provide our perspectives on the challenges presented by these developments and how SBML Level provides the foundation needed to support this evolution. 3

Christian Bunse - One of the best experts on this subject based on the ideXlab platform.

  • Design verification in model-based μ-controller development using an abstract component
    Software & Systems Modeling, 2011
    Co-Authors: Yunja Choi, Christian Bunse
    Abstract:

    Component-based software development is a promising approach for controlling the complexity and quality of software systems. Nevertheless, recent advances in quality control techniques do not seem to keep up with the growing complexity of embedded software; embedded systems often consist of dozens to hundreds of software/hardware components that exhibit complex interaction behavior. Unanticipated quality defects in a component can be a major source of system failure. To address this issue, this paper suggests a design verification approach integrated into the model-driven, component-based development methodology M armot . The notion of abstract components—the basic building blocks of M armot —helps to lift the level of abstraction, facilitates high-level Reuse, and reduces verification complexity by localizing verification problems between abstract components before refinement and after refinement. This enables the identification of unanticipated design errors in the early stages of development. This work introduces the M armot methodology, presents a design verification approach in M armot , and demonstrates its application on the development of a  μ -controller-based abstraction of a car mirror control system. An application on TinyOS shows that the approach helps to Reuse Models as well as their verification results in the development process.

  • Design verification in model-based μ-controller development using an abstract component
    Software & Systems Modeling, 2010
    Co-Authors: Yunja Choi, Christian Bunse
    Abstract:

    Component-based software development is a promising approach for controlling the complexity and quality of software systems. Nevertheless, recent advances in quality control techniques do not seem to keep up with the growing complexity of embedded software; embedded systems often consist of dozens to hundreds of software/hardware components that exhibit complex interaction behavior. Unanticipated quality defects in a component can be a major source of system failure. To address this issue, this paper suggests a design verification approach integrated into the model-driven, component-based development methodology Marmot. The notion of abstract components--the basic building blocks of Marmot--helps to lift the level of abstraction, facilitates high-level Reuse, and reduces verification complexity by localizing verification problems between abstract components before refinement and after refinement. This enables the identification of unanticipated design errors in the early stages of development. This work introduces the Marmot methodology, presents a design verification approach in Marmot, and demonstrates its application on the development of a μ-controller-based abstraction of a car mirror control system. An application on TinyOS shows that the approach helps to Reuse Models as well as their verification results in the development process.