phraSED-ML: A paraphrased, human-readable adaptation of SED-ML

J Bioinform Comput Biol. 2016 Dec;14(6):1650035. doi: 10.1142/S0219720016500359. Epub 2016 Sep 30.


Motivation: Model simulation exchange has been standardized with the Simulation Experiment Description Markup Language (SED-ML), but specialized software is needed to generate simulations in this format. Text-based languages allow researchers to create and modify experimental protocols quickly and easily, and export them to a common machine-readable format.

Results: phraSED-ML language allows modelers to use simple text commands to encode various elements of SED-ML (models, tasks, simulations, and results) in a format easy to read and modify. The library can translate this script to SED-ML for use in other softwares.

Availability: phraSED-ML language specification, libphrasedml library, and source code are available under BSD license from .

Keywords: SBML; SED-ML; reproducibility; simulation.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Computer Simulation
  • Extracellular Signal-Regulated MAP Kinases / metabolism
  • Models, Theoretical*
  • Programming Languages*
  • Software
  • Stochastic Processes
  • Systems Biology / methods*


  • Extracellular Signal-Regulated MAP Kinases