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Category Archives: Pathways
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
Posted in General Interest, LaTeX, Pathways, Publishing, Textbooks
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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
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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:
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import tellurium as te import roadrunner r = te.loada(""" $Xo -> S1; k1*Xo; S1 -> S2; k2*S1; S2 -> S3; k3*S2; S3 -> $X1; k4*S3; k1 = 0.1; k2 = 0.4; k3 = 0.5; k4 = 0.6; Xo = 1; """) print r.getFullStoichiometryMatrix() |
Running this script by clicking on the green arrow in the tool bar will yield:
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_J0, _J1, _J2, _J3 S1 [[ 1, -1, 0, 0], S2 [ 0, 1, -1, 0], S3 [ 0, 0, 1, -1]] |
Posted in Modeling, Pathways, SBML, Systems Theory
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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
Posted in Modeling, Pathways, SBML, 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
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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
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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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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
Posted in LaTeX, Modeling, Pathways, Programming, Publishing
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