Taverna services for Systems Biology



If you have any questions, comments or seek help with our WS or any other resource, please contact us via tav4sb discussion group or directly at tav4sb@mimuw.edu.pl.

Simulate SBML-derived ODEs

This is a simple ODEs numerical simulation experiment for the enzymatic reaction deterministic model (SBML). ODEs are derived automatically, based on SBML-encoded rate laws for reactions.

Depiction of the "Simulate SBML-derived ODEs" workflow.

"Simulate SBML-derived ODEs" workflow

To run this experiment's workflow choose File > Open workflow location... and copy-paste the following link to the workflow file. Then, File > Run workflow... and wait for results. This workflow has no inputs - all simulation and plot parameters are embedded in string constants (modelUrl, simTime, simTimepointsNr and plotMarkersOpt, plus filterVariables/regex default value). That's what you should change if you want to play around. In particular, there is only one plotting option given, which says not to plot data points markers.
Note: For description of plotting options check mathPlot WS operation wrapper docs on optionList input at myExperiment or input docs at BioCatalogue.

As a result of running this experiment you should get the <timepoints> XML element with simulated values of SBML species variables over 30 seconds, and the following plot of these time points:
Numerical simulation of the enzymatic reaction model ODEs.

From the plot you can see that the system stabilizes in approximately 25 seconds with the peak activity at 2nd second, when most of the enzymes are at work, being involved with substrate in a complex, which, in turn, converts substrate to the product.


Taverna 2 workflow files: