Category Archives: Pathways

How do I run a stochastic simulation using Tellurium/libRoadRunner?

In this post I will show you how to run a stochastic simulation using our Tellurium application. Tellurium is a set of libraries that can be used via Python. One of those libraries is libRoadRunner which is our very fast … Continue reading

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Computing the steady state using Tellurium

If you’re building a model and you want to quickly find the model’s steady state, you can call the command steadyState. Let’s illustrate this with an example: import tellurium as te r = te.loada (”’ # Define a simple linear … Continue reading

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Bifurcation Analysis with Tellurium

I thought I’d try and write a series of HowTos on Tellurium, our python based tool for the construction, simulation and analysis of biochemical models. Details on this tool can be found here. One the unique features of Tellurium is … Continue reading

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Tikz Code for Drawing Metabolic Feedback Loops

I needed some figures that displayed a variety of different negative feedback loops so I created these using Tikz. Nothing particularly special. There are some absolute distances in the code which perhaps could be removed to make it more generic. … Continue reading

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New Modeling Book Published

I am happy to announce the publication of my new book this March: Essentials of Biochemical Modeling. Computer models of biochemical systems are starting to play an increasingly important role in modern systems and synthetic biology. This monograph introduces students to … 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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Announce: release of libRoadRunner 1.0.0

After a lot of work I am pleased to announce the first official release of libRoadRunner, 1.0.0. This represents a complete rewrite of the original C# RoadRunner developed by Frank Bergmann and Herbert Sauro. libRoadRunner is a high-performance cross-platform C/C++ library that supports … Continue reading

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Bottlenecks and Slow Steps – again

I’ve written a few articles on this blog about the irrationality of bottlenecks and slow steps in metabolism, hoping that one day my fellow scientists will feel the same. Sadly it is not true and maybe I should write more … Continue reading

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Whole Cell Models

We’ve seen in the last couple of years increased interest in building whole cell models, that is computer models that attempt to simulate a whole organism. The most recent attempt was by Karr et al, published in Cell, 2012, 150(2), … 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.

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