New Text Book
Enzyme Kinetics for Systems Biology is a modern text book for undergraduate classes or as a reference text in systems and synthetic biology. The text covers all the main topics in enzyme kinetics including chapters on the kinetics of gene expression and generalized rate laws. Available now at the special price of only $39.95. Purchase at Amazon Special student and bulk order prices available at blog.analogmachine.org
Category Archives: Enzyme Kinetics
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
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
Crowd Funding: Microryza
There is a new crowd funding site has just started that specializes in funding research. Called Microryza, the organization aims to focus on funding risky research projects or educational outreach efforts. Yours truly submitted one of the first projects (no affiliation to the … Continue reading
Jim Burns’ Ph.D Thesis
Why on earth should anyone would want to download a Ph.D thesis that is now almost 40 years old and presumably way out of date and completely irrelevant in today’s terabyte data world? Well for one, Jim’s thesis is an … Continue reading
It’s Christmas!
It’s Christmas, term is winding down at the University, the students are going home and than means spare time to do something other than official work. Here is a small Windows App I wrote that simulates a simple enzyme mechanism. … Continue reading
Posted in Enzyme Kinetics, Pathways, Systems Theory
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Modeling Webinar Hosted by Rosa
Modeling Webinar I will be presenting a Webinar hosted by Rosa to be held on Tuesday 26th of July at 12:00 to 1:00 pm EDT on Standards and Software in Biomedical Systems Modeling. Register here if you wish to attend … Continue reading
SBML Parts Decomposition Tool
Biochemical Pathway Component Finder Ever wanted to extract a particular enzyme or reaction from a computational model? Perhaps not, but those of you who have, there is now a tool available to do that very task. Maxwell Neal from University … Continue reading
Posted in Enzyme Kinetics, General Science Interest, Modeling, Pathways, SBML
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Systems Thinking in Systems Biology: Part 2
In the last post I posed the question, what would happen to a metabolic pathway if we added an inhibitory drug to the middle enzyme in a linear sequence of steps? Here is the answer. Take a sequence of enzymes … Continue reading
Posted in Enzyme Kinetics, Molecular Biology, Pathways, Systems Theory
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Systems Thinking in Systems Biology: Part 1
Let’s say we inhibit an enzyme in a metabolic pathway by perhaps reducing the expression of the gene that makes the enzyme or more easily by adding a drug that inhibits the enzyme.What do you think will happen? When I … Continue reading
Proportional and Relative Changes
There is an excellent description of the difference between logarithmic and linear scales in the book “Mathematical Analysis for Economists” by R Allen which I describe here. Consider the following two sequences of numbers: 100, 150, 200, 250, 300, 100, … Continue reading
Posted in Enzyme Kinetics, Math
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