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Category Archives: Software
Plotting Bar graph of Species Concentrations 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
Posted in Modeling, Pathways, Programming, Python, Software, Tellurium
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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
Posted in General Science Interest, Math, Modeling, Pathways, Programming, Software
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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
Posted in Modeling, Pathways, Programming, SBML, Software, Systems Theory
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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:
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v1: $Xo -> S1; k1*Xo; v2: S1 -> S2; k2*S1*S2^h/(10 + S2^h) + k3*S1; v3: S2 -> ; k4*S2; |
In this model S2 … Continue reading
Posted in Modeling, Pathways, Programming, Software, Systems Theory
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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
Posted in Modeling, Pathways, Programming, SBML, Software
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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:
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import tellurium as te r = te.loada (''' # Define a simple linear chain of reactions $Xo -> S1; k1*Xo; S1 -> S2; k2*S1; S2 -> S3; k3*S2; S3 -> $X1; k4*S3; # Initialize rate constants k1 = 0.2; k2 = 0.7; k3 = 0.15; k4 = 1.3; Xo = 10 ''') print r.getSteadyStateValues() |
Running this script by clicking in the green arrow in the tool … Continue reading
Posted in Modeling, Pathways, Software
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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
Posted in General Science Interest, Modeling, Pathways, Software
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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
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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
Posted in Programming, Software
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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
Posted in Delphi, Programming, SBML, Software
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