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SBMLSimulator

Simulates an SBML model using SBML ODE Solver.

Tip: you may need to try the CVS development version of SBML ODE Solver if the latest official release does not work. This can be done with "cvs -z3 -d:pserver:anonymous@sbmlsolver.cvs.sourceforge.net:/cvsroot/sbmlsolver co -P SBML_odeSolver" (or similar; see the SOSlib web site for details). You need to install the Sundials library first. Try the latest version.

Version 1.2
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Authors Kristian Ovaska (kristian.ovaska@helsinki.fi)
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Requires R ; SBML ODE Solver (SOSlib)
Source files component.xml SBMLSimulator.r
Usage Example with default values

Inputs

Name Type Mandatory Description
in SBML Mandatory SBML model. SBML Level 1 and Level 2 are supported.

Outputs

Name Type Description
plot Latex Plots of molecular species as a function of time. All species are in the same plot. Start time, end time and list of species are configured using parameters.
timepoints Matrix Amounts of species at various time points. The first column, t, marks the time. The other columns mark the molecular amounts of each species at the time point.

Parameters

Name Type Default Description
endTime float 1 End time for simulation and reporting.
includeSpecies string "*" Comma-separated list of molecular species IDs that are to be included in the outputs. These correspond to the id attribute in the SBML file. The special value * includes all species.
legendColumns int 1 Number of columns in the legend. The default (1) creates a vertical legend.
legendPosition string "topright" Position of the legend box. One of "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right" and "center".
odeSolverExecutable string "odeSolver" Name of the SBML ODE Solver executable.
plotTitle string "" Title of the time series plot.
reportStep int 1000 Number of time points to report. Increasing this number does not increase integration accuracy, but does increase the accuracy of handling SBML events.
sectionType string "section" Type of LaTeX section: usually one of section, subsection or subsubsection.
startTime float 0 Start time for reporting.
yLog boolean false True if the Y axis should be in logarithmic scale, false if linear scale.

Test cases

Test case Parameters IN
in
OUT
plot
OUT
timepoints
case1 (missing) in (missing) (missing)
case2 properties in (missing) (missing)

includeSpecies=MKKK_P,MKK_PP,MAPK_PP,
yLog=true,
legendPosition=topright,
legendColumns=3,
startTime=2,
endTime=7.5,
reportStep=100

case3 (missing) in (expecting failure) (expecting failure)

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