Category Archives: Pathways

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

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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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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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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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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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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

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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

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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

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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

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