Category Archives: Software

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 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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Bode Plots using Python

I needed a quick way to plot some Bode plots for a second order system. I didn’t have access to Matlab, instead I searched for a solution using Python, and I found one. Documentation is a bit sparse  so this … Continue reading

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Programming Language Popularity

As programmers we sometimes like to play the game of what is the most popular programming language? There are various metrics online that try to measure this, most notably TIOBE, PYPL and Trendy Skills. They are all flawed in someway and often … Continue reading

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My First Mac OS Application

I finished my first Mac OS application. Two screenshots are shown below, I’ll be making it available download at the end of the week. This was a test application to see how easy it would be use write a portable … Continue reading

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Windows 10: Finally a better console

The windows console (accessed via cmd) is the coelacanth of software, barely unchanged though millions of years of software evolution. But finally selection pressure has final created a new species. Today Microsoft announced the start of the Windows 10 build … Continue reading

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