Tag Archives: compsci

A simulating winter!

By Daniel | Published: January 26, 2012

That’s a graph automatically generated by the cell signalling pathway simulation automation software I developed over the winter break. It’s a bit ugly — a quick and dirty CDF rendered in R of activation times of ERK in the TCR (T-Cell Receptor) pathway model for a particular endogenous pMHC ligand dosage. Fancy lingo, eh? The [...]

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Nucleotides are nice, but codons are capital!

By Daniel | Published: December 13, 2011
borrelia_plasmid_protein2

I’ve updated my OpenGL DNA renderer to support amino acids, rather than just single nucleotides. I find these colorful DNA representations oddly aesthetically pleasing, so I’m pursuing it a bit further. It’s always possible I’ll find utility in being able to do some unique sequence rendering. I borrowed the color scheme for amino acids from [...]

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Pronounced Plasmids

By Daniel | Published: December 10, 2011
borellia_plasmid_spiral

Several months ago I posted a maze I generated in C++ with OpenGL. Being pre-occupied with molecular biology lately, I took my old code out and adapted the concept for rendering a bacterial plasmid. Specifically, this little beauty is: Borrelia valaisiana VS116 plasmid VS116_cp9, complete sequence. The generative sequence renders quads around in a spiral, [...]

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Made a maze.

By Daniel | Published: April 14, 2011

Maze generated in c++ using disjoint set (union by rank with path compression), random wall smashing, and opengl to render each cell with quads. These are simple, yet so pretty, like traditional Chinese lattice design.

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