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
Monthly Archives: May 2011
MAPK: Feedback Amplifier, Part 2
In part 1 of this series, a brief history of negative feedback was given. Here we will look at the advantages and disadvantages of negative feedback, particularly in relation to signal transmission. Amplifiers Amplifiers used by electrical engineers are designed to magnify the … Continue reading
MAPK: Feedback Amplifier, Part I
A recent paper by Sturm et al., report results that support the hypothesis that the MAPK cascade acts as a negative feedback amplifier. The systems biology literature is full of reviews and articles about oscillators and bistable systems and very little else other than … Continue reading
Drawing Pathways with TikZ: Part 2
Timo Maarleveld, as part of his thesis writing, started using TikZ to draw some of his network diagrams. To give you an example, the figure below was generated by the code listed at the end. IT gives some idea of … Continue reading
Posted in LaTeX, Pathways, Publishing
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Useful LaTex Documents
Here are some very useful documents on LaTeX that I have come across over the years: 1. Comprehensive Symbol List The comprehensive symbol list includes 5913 symbols and the corresponding LaTeX command by Scott Pakin 2. Math Mode A highly … Continue reading
Posted in LaTeX, Math
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Top 10 LaTeX Packages
These are the 10 most common packages I use in my LaTeX documents. 1. amsmath, amsfonts Particularly handy for rendering matrices. amsmath has a set of tailored matrix environments. For example here are three examples that use pmatrix, bmatrix … Continue reading
Posted in LaTeX, Publishing
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Symbolic MCA
Many years ago, Simon Thomas and David Fell (1) wrote a program called MetaCon that could compute the control coefficient equations given an arbitrary network. At the time it was very useful but for various reasons it could not be … Continue reading
Posted in LaTeX, Pathways, Systems Theory
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Sun Dogs in Seattle
Here is a photograph I took of a small sun dog that I spotted from my house in Seattle on the evening of May 11, 2011. In the image you will see a ‘mock’ sun to the left of the … Continue reading
Posted in General Science Interest
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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
Drawing Pathways with TikZ: Part 1
Drawing biochemical pathway diagrams has never been easy. Many of us probably use a combination of Power Point, illustrator, Inkscape, or even MS Paint. Of these Illustrator and Inkscape are probably the most useful but Illustrator is expensive and Inkscape … Continue reading
Posted in LaTeX, Pathways
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