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

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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

Posted in General Science Interest, Molecular Biology, Pathways, Systems Theory | 2 Comments

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 | 1 Comment

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

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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

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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

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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

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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 | 1 Comment

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

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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

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