Category Archives: Systems Theory

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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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

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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:

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:

Running this script by clicking on the green arrow in the tool bar will yield:

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How to do a simple simulation using Tellurium

The most common requirement is the ability to carry out a simple time course simulation of a model. Consider the model:     Two reactions and three metabolites, S1, S2 and S3. We can describe this system using an Antimony … Continue reading

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Bode Plots using Python

I needed a quick way to plot some Bode plots for a second order system. I didn’t have access to Matlab, instead I searched for a solution using Python, and I found one. Documentation is a bit sparse  so this … Continue reading

Posted in General Science Interest, Modeling, Programming, Software, Systems Theory | 1 Comment

Skynet Edges Closer

There is a fascinating article in science this week about the construction in hardware of a neural chip. This isn’t a new idea but scale and flexibility is novel. The chip is made by researchers from IBM and Cornell and can … Continue reading

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Reversibility and Product Inhibition

It is common in biochemistry to categorize reactions as either reversible or irreversible. What do we mean by these terms? Let’s look at a simple reaction such as:     where A is transformed to B. The rate of reaction … Continue reading

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Synthetic Biology: It’s an analog world

I significant paper on synthetic biology got published this week by an innovative group from MIT (Daniel et al). Read our News and Views article that discusses the importance of the paper.

Posted in General Science Interest, Molecular Biology, Pathways, Synthetic Biology, Systems Theory | Leave a comment

Linear Dynamics Application

There are a number of online apps that can show students the phase plane dynamics of a 2d system. Notable examples include: Phase Portrait Viewer from the d’Arbeloff Interactive Math Project – requires Java installed Wolfram Phase Portrait Viewer – … Continue reading

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