Up: Component summary
Up: Component summary
Component
SBMLSimulatorSimulates 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 |
|---|---|
| Bundle | tools |
| Categories | Pathway |
| Authors | Kristian Ovaska (kristian.ovaska@helsinki.fi) |
| Issue tracker | View/Report issues |
| 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, |
||||||
| case3 | (missing) | in | (expecting failure) | (expecting failure) | ||