# Category Archives: Programming

## 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

## 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

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

## 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

## 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