Abstract
AbstractThe Simulation Experiment Description Markup Language (SED-ML) is a XML format describing simulation experiments, so that they can be easily exchanged independent of software tools that created them. This document describes the SED-ML Script, a Python based shorthand that makes it easy to create / edit SED-ML documents.
Highlights
The Simulation Experiment Description Markup Language (SED-ML) is a XML format describing simulation experiments, so that they can be exchanged independent of software tools that created them
The following describes the list of functions available in SED-ML Script
Example: The id to give the new simulation experiment A KISAO identifier that describes the simulation algorithm used A double representing the start time for the simulation A double representing the time when to start collecting data The end time, or the time when to stop the simulation An integer value equal to the number of data points to collect between the initialTime and the endTime
Summary
The Simulation Experiment Description Markup Language (SED-ML) is a XML format describing simulation experiments, so that they can be exchanged independent of software tools that created them. The following describes the list of functions available in SED-ML Script. The following describes a simulation ‘simulation1’ carried out with the CVODE ode solver to simulate from time 0 to 500, collecting 1000 output points. AddModel(modelId, source, language) Parameters: modelId source language Example: The id to give the new model The source where to find the model, this can be a reference to a local file, a url or a Miriam uri, or an id of another model The language of the model (defaults to urn:sedml:language:sbml). A model defined from a web address: AddModel('model1', 'http://www.ebi.ac.uk/biomodels/modelsmain/publ/BIOMD0000000012/BIOMD0000000012.xml', 'urn:sedml:language:sbml'). A model by Miriam Uri (using the default language): AddModel('model1', 'urn:miriam:biomodels.db:BIOMD0000000139').
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