Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1

  • 1 University of Washington, Seattle, USA
  • 2 Eight Pillars Ltd, Edinburgh, UK
  • 3 University of Heidelberg, Heidelberg, Germany
  • 4 Newcastle University, Newcastle, UK
  • 5 University College London, London, UK
  • 6 Humboldt-University Berlin, Berlin, Germany
  • 7 University of Utah, Salt Lake City, USA
  • 8 QSP Simcyp, Sheffield, UK
  • 9 California Institute of Technology, Pasadena, USA

Abstract

Biological models often contain elements that have inexact numerical values, since they are based on values that are stochastic in nature or data that contains uncertainty. The Systems Biology Markup Language (SBML) Level 3 Core specification does not include an explicit mechanism to include inexact or stochastic values in a model, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactic constructs. The SBML Distributions package for SBML Level 3 adds the necessary features to allow models to encode information about the distribution and uncertainty of values underlying a quantity.

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Journal + Issues

The Journal of Integrative Bioinformatics is an international journal dedicated to methods and tools of computer science and electronic infrastructure applied to biotechnology. The journal covers mainly but not exclusively data/method integration, modeling, simulation and visualization in combination with applications of theoretical/computational tools and any other approach supporting an integrative view of complex biological systems.

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