Author Archives: hsauro

Front-Loading of Flux Control

There is an interesting property that straight chain pathways have which I call front-loading. The phenomenon has been known for some time and I describe it in detail in my recent textbook on Metabolic Control Analysis. Let’s say we have … Continue reading

Posted in Enzyme Kinetics, Metabolic Control Analysis, Modeling, Pathways, Programming, Python, Systems Theory, Tellurium | Leave a comment

Stream Plots Using Tellurium

Every wanted to do a phase plot for a toggle switch or any two-dimensional model? Here is an example of using a stream plot combined with SBML models using Tellurium based on a simple toggle switch.

The colored circles … Continue reading

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Marsaglia’s MWC (multiply with carry) Random Number Generator for Object Pascal

In the past, I’ve tended to use the Mersenne Twister for generating pseudo-random numbers. This is a widely used generator because it has a very long period of 2^{19937} – 1. The one issue is that it’s not the fastest … Continue reading

Posted in General Interest, General Science Interest, Math, Programming, Software | Leave a comment

A simple bistable system

Here is a simple bistable system I sometimes use in class. I like it because it’s easy to explain plus the addition of one extra reaction turns it into a relaxation oscillator. If you run the above code you’ll get: … Continue reading

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Simulate Regular Doses using Antimony/SBML in the Tellurium Python Tool

Someone recently asked how to create a model where a molecular species received a regular dose at a fixed interval of 12 hours. They wanted something where a species A is being degraded but at regular intevals is increased by … Continue reading

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One of my best friends passed away today

It is with enormous and deep sorrow that one of my best friends in the world passed away today as a result of Hemangiosarcoma. This is where the spleen becomes cancerous which eventually results in fatal hemorrhaging. There is virtually … Continue reading

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Generating log ranges in Python

This is a very short blog on how to generate logarithmic ranges in python: import numpy as np # Brute force x = [0.1, 1, 10, 100, 1000] # Classic explicit loop x = 0.1 for i in range (5): … Continue reading

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Explaining the smallest chemical network that can display a Hopf bifurcation

Last year I did a short blog on simulating the smallest chemical network that could display Hopf bifurcation oscillations. Here I want to revisit this with an eye to explain why it oscillates. The paper in question is Wilhelm, Thomas, … Continue reading

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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

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New Textbook on Metabolic Control Analysis

New Textbook Published I am pleased to announce the publication of my new textbook: Introduction to Metabolic Control Analysis   “This book is an introduction to control in biochemical pathways. It introduces students to some of the most important concepts … Continue reading

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