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Category Archives: Pathways
C Based Reduce Row Echelon Code
I recently needed some code to compute the reduced row echelon of a matrix. Applications such as Matlab, Mathematics, sympy and R support this functionality out of the box. Libraries such as LAPACK do not, including the linear algebra package … Continue reading
Posted in Modeling, Pathways, Programming, Software
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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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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
Posted in General Science Interest, LaTeX, Pathways, Programming, Textbooks
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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
Posted in General Interest, LaTeX, Pathways, Programming, Publishing, Textbooks
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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
Posted in General Interest, LaTeX, Modeling, Pathways, Programming, Publishing
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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
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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