Literature DB >> 23715987

Supporting SBML as a model exchange format in software applications.

Sarah M Keating1, Nicolas Le Novère.   

Abstract

This chapter describes the Systems Biology Markup Language (SBML) from its origins. It describes the rationale behind and importance of having a common language when it comes to representing models. This chapter mentions the development of SBML and outlines the structure of an SBML model. It provides a section on libSBML, a useful application programming interface (API) library for reading, writing, manipulating and validating content expressed in the SBML format. Finally the chapter also provides a description of the SBML Toolbox which provides a means of facilitating the import and export of SBML from both MATLAB and Octave ( http://www.gnu.org/software/octave/) environments.

Mesh:

Year:  2013        PMID: 23715987     DOI: 10.1007/978-1-62703-450-0_11

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  6 in total

1.  Requirements for the formal representation of pathophysiology mechanisms by clinicians.

Authors:  B de Bono; M Helvensteijn; N Kokash; I Martorelli; D Sarwar; S Islam; P Grenon; P Hunter
Journal:  Interface Focus       Date:  2016-04-06       Impact factor: 3.906

Review 2.  Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems.

Authors:  Lily A Chylek; Leonard A Harris; Chang-Shung Tung; James R Faeder; Carlos F Lopez; William S Hlavacek
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2013-09-30

3.  Snoopy's hybrid simulator: a tool to construct and simulate hybrid biological models.

Authors:  Mostafa Herajy; Fei Liu; Christian Rohr; Monika Heiner
Journal:  BMC Syst Biol       Date:  2017-07-28

4.  Synthetic biology tools for engineering Goodwin oscillation in Trypanosoma brucei brucei.

Authors:  Yanika Borg; Sam Alsford; Vasos Pavlika; Alexei Zaikin; Darren N Nesbeth
Journal:  Heliyon       Date:  2022-02-03

5.  R-based software for the integration of pathway data into bioinformatic algorithms.

Authors:  Frank Kramer; Michaela Bayerlová; Tim Beißbarth
Journal:  Biology (Basel)       Date:  2014-02-07

6.  MAGPIE: Simplifying access and execution of computational models in the life sciences.

Authors:  Christoph Baldow; Sebastian Salentin; Michael Schroeder; Ingo Roeder; Ingmar Glauche
Journal:  PLoS Comput Biol       Date:  2017-12-15       Impact factor: 4.475

  6 in total

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