Category Archives: Pathways

Bifurcation Analysis with Tellurium

Posted on October 28, 2016 by hsauro

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

Posted on October 15, 2016 by hsauro

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 →

Posted in LaTeX, Modeling, Pathways, Programming, Publishing | Leave a comment

New Modeling Book Published

Posted on April 2, 2014 by hsauro

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

Posted on March 28, 2014 by hsauro

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

Posted on December 19, 2013 by hsauro

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 →

Posted in Modeling, Pathways, Programming, SBML, Software | Leave a comment

Bottlenecks and Slow Steps – again

Posted on October 28, 2013 by hsauro

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

Posted on October 24, 2013 by hsauro

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

Posted on May 17, 2013 by hsauro

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

Drawing Pathways with Tikz

Posted on May 8, 2013 by hsauro

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

Posted on March 23, 2013 by hsauro

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 →

Posted in Enzyme Kinetics, General Science Interest, Metabolic Control Analysis, Modeling, Molecular Biology, Pathways, Systems Theory | Leave a comment