Category Archives: Programming

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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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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Z80 Microcomputer

Its been a while since I wrote something for this blog, mainly due to pressures of work. However its summer now and I’ve managed to carve out some time to do other work related projects. One thing I’ve done in … 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

Posted in General Science Interest, Modeling, Programming, Software, Systems Theory | 1 Comment

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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Simple RK4 Code

Thought I’d start off the New Year with a simple freebie, a 4th Order Runge-Kutta class for Delphi, Windows and Mac OS. Should also work on Android and iOS mobile platforms and with Free Pascal. The code below shows how … Continue reading

Posted in Delphi, Modeling, Programming | 1 Comment

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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