Category Archives: Pathways

Plotting Bar graph of Species Concentations in Tellurium

I had a model with 27 flaoting species and I wanted to plot the steady state concentrations on a histogram where the labels were the names of the different species. Here is a general purpose script that will do that: … Continue reading

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Multilayered Cascade using TikZ

A summer student working in my lab, Ming Hong Lui from Hong Kong University (HKUST), worked on the perturbation analysis of signaling cascades and in his writeup he use TikZ to draw a nice cascade diagram which I present here. … Continue reading

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Another Inhibition Pathway Diagram using TikZ

Here is another pathway diagram I needed to draw using TikZ. IN this case I needed an inhibited step. This was more tricky because I needed the inhibition line to point midway to a reaction but without touching the reaction … Continue reading

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Drawing a Pathway Fragment with Inhibition using Tikz

Here is another quick pathway fragment I needed today. This won’t scale well because I’ve used some fixed dimensions eg the width of the lines and the size of the text. But these are easily adjusted if you want to … Continue reading

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Drawing a ‘Futile’ Cycle using Tikz

I was in need of a diagram of a futile cycle. I tried illustator but I didn’t have the right LaTeX fonts so the figure did blend well with the rest of the document. I decided to make one using … Continue reading

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Plotting 3D graphs using Python and Tellurium

As an example I wanted to show how one could plot a 3D phase plot. A great example to use for this is the Lorenz Attractor. This system is interesting because it displays chaotic behavior. The differential equations for the … Continue reading

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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 Tellurium

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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