Category Archives: Systems Theory

Irreversible Bistability

Last week I was in need of an irreversible bistable switch to show my class. I remember seeing one in the well known review by Tyson et al, Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in … Continue reading

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Michael Savageau’s Book in Print Again

I’ve been meaning to mention this for some time but Michael Savageau book, ‘Biochemical Systems Analysis’ is available in print again in the form of a paperback from amazon for only $29.95. I grew up with this book as an … Continue reading

Posted in Enzyme Kinetics, Metabolic Control Analysis, Systems Theory, Textbooks | Leave a comment

Building an Analog Integrator

Something I’ve been wanting to do for a while was is to build a simple analog integrator. Here is my first attempt. I bread-boarded the circuit first to get it working then made it more permanent and stable by soldering … Continue reading

Posted in Electronics, General Science Interest, Systems Theory | 1 Comment

Electronic Gene Circuit

The figure below shows a single unit from the Microryza gene network circuit project. The circuit models a transcription factor that acts as a repressor. The output from the circuit is the level of protein which can be fed into … Continue reading

Posted in Electronics, Enzyme Kinetics, General Science Interest, Modeling, Molecular Biology, Synthetic Biology, Systems Theory | Leave a comment

Misconceptions in Metabolism II

A week ago I wrote about some misconceptions in metabolism that arose from a trip to a systems biology workshop in Holland. This week I discovered that Nature is perpetrating similar misconceptions in their News and Views section. I came … Continue reading

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Misconceptions in Metabolism

I’m currently at the ISGSB meeting (International Study group for Systems Biology – formally BTK) in Holland. This is a group that values both theoretical analysis and experimentation in biochemical network analysis. Its an interesting group of people that I have literally … Continue reading

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Default Compartments in SBML

A reoccurring problem that I’ve had with SBML since day one is how to deal with a default compartment. Take for example a visual design tool such as JDesigner. At start up it creates an implicit compartment represented by the empty canvas. … Continue reading

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Ludicrous as it may sound

I was reminded the other day of an interesting quote from a 2000 FEBS paper which starts with: “How highly would one rate an economic analysis of a factory that ignored the consumer demand for its products? Ludicrous as it … Continue reading

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Why are Systems Biologists so bad at Computer Modeling?

The title of this blog is meant to be a little brazen and eye catching but I decided to write it after having been on a variety of government grant panels over the years where I am always shocked at the … Continue reading

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NCI Partners with the DREAM Project

Two acronyms in one title, translated the title says: The National Cancer Institute Partners with the Dialogue for Reverse Engineering Assessments and Methods. Perhaps not much help but actually this is a great idea. The National Caner Institute is partnering with … Continue reading

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