Author Archives: hsauro

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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How do I run a stochastic simulation using Tellurium/libRoadRunner?

In this post I will show you how to run a stochastic simulation using our Tellurium application. Tellurium is a set of libraries that can be used via Python. One of those libraries is libRoadRunner which is our very fast … Continue reading

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Computing the steady state using Tellurium

If you’re building a model and you want to quickly find the model’s steady state, you can call the command steadyState. Let’s illustrate this with an example: import tellurium as te r = te.loada (”’ # Define a simple linear … Continue reading

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Bifurcation Analysis with Tellurium

I thought I’d try and write a series of HowTos on Tellurium, our python based tool for the construction, simulation and analysis of biochemical models. Details on this tool can be found here. One the unique features of Tellurium is … Continue reading

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Tikz Code for Drawing Metabolic Feedback Loops

I needed some figures that displayed a variety of different negative feedback loops so I created these using Tikz. Nothing particularly special. There are some absolute distances in the code which perhaps could be removed to make it more generic. … Continue reading

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The Confusion of Modern Textbooks – Stylistic Sugar

I’ve been looking for a textbook on statistics for a class I’ll teach in the autumn term. While the content of many textbooks might be ok the way the information is presented makes them difficult to read – at least … Continue reading

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Transistor Based Flip-Flop or a (not)RS NAND Latch

Been a while since I did a posting, too much time spent writing grants, and I mean a lot of time. In this blog I thought I’d describe a small project I did a month or two ago to build … Continue reading

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