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: Pathways
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
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
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
Posted in Modeling, Pathways, SBML, Software, Systems Theory
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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
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
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
Genetic XOR Circuit
The synthetic biology community has implemented many logic gates in vivo using various genetic components. Two less common gates are the XOR and XNOR functions. The truth table for the XOR function is shown below: The XOR function operates such … 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 Course at Indiana University
Not that kind of modeling, but the kind that involves building computational models of biochemical networks and multicellular systems. James Glazier, the Director of the Biocomplexity Institute at Indiana University is the lead organizer behind a series of workshops that … Continue reading
Posted in General Science Interest, Modeling, Molecular Biology, Pathways, SBML, Software
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