Monthly Archives: November 2016

How do I change the simulation tolerances in Tellurium?

For very complicated and large models it may be necessary to adjust the simulator tolerances in order to get the correct simulation results. Sometimes the simulator will terminate a simulation because it was unable to proceed due to numerical errors. … Continue reading

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How do I plot phase plots using Tellurium?

Phase plots are a common way to visualize the dynamics of models where time courses are generated and one variable is plotted against the other. For example consider the following model that can show oscillations: v1: $Xo -> S1; k1*Xo; … Continue reading

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How to get the Stoichiometry Matrix using Tellurium

Here is a simple need, given a reaction model how do we get hold of the stoichiometry matrix? Consider the following simple model: import tellurium as te import roadrunner r = te.loada(“”” $Xo -> S1; k1*Xo; S1 -> S2; k2*S1; … Continue reading

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How to do a simple simulation using Telluirum

The most common requirement is the ability to carry out a simple time course simulation of a model. Consider the model:     Two reactions and three metabolites, S1, S2 and S3. We can describe this system using an Antimony … Continue reading

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