Category Archives: Pathways

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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Drawing Pathways with Tikz

I had the need to draw a negative feedback around a linear pathway. Normally I would use a vector drawing packages to do this, such as Illustrator or Inkscape. This time I thought I would try the tikz package that … Continue reading

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Choke points, Load points, Hots spots and Key steps

Choke points, load points, hot spots, key steps and critical steps are some of the many phrases that have been coined to describe places in a biochemical network where perturbations are said to make a difference. Locating these places is … Continue reading

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