# Category Archives: Software

## Simple Stochastic Code in Python

It’s been a while since I blogged (grant writing etc gets int he way of actual thinking and doing) so here is a quick post that uses Python to model a simple reaction A -> B using the Gillespie next … Continue reading

## How to do a simple parameter scan using Tellurium

A common task in modeling is to see how a parameter influences a model’s dynamics. For example, consider a simple two reaction pathway: -> S1 -> where the first reaction has a fixed input of vo and the second reaction … Continue reading

## How to plot a grid of phase plots using Tellurium

Let’s say we have a chemical network model where the species oscillate and you’d like to plot every combination of these on a grid. If so, then this code might be of help.

This code will generate: Here is … Continue reading

## Smallest Chemical Reactions Systems that is Bistable

A while back Thomas Wilhelm, published a paper that described the smallest chemical network that could display bistability. The paper that describes this result is: Wilhelm, T. (2009). The smallest chemical reaction system with bistability. BMC systems biology, 3(1), 90. … Continue reading

## Smallest Chemical Reaction System with Hopf Bifurcation

A while back Wilhelm, and Heinrich published a paper that described the smallest chemical network that could display a Hopf bifurcation. That is, the chemical species oscillated. The paper that describes this result is: Wilhelm, Thomas, and Reinhart Heinrich. “Smallest … Continue reading

## 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

## 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

## 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

## 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