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 [...]

Posted in Uncategorized| Also tagged , , , , | 1 Response

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 [...]

Posted in Uncategorized| Also tagged , | Leave a comment

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, [...]

Posted in Uncategorized| Also tagged , | Leave a comment

  • The Native Inhabitant:

    Web and IT pro turned novice scientist. Currently studying computer science and bioinformatics at Hunter College.

    Here be: dragons, bio + engineering + medicine + ethics, vegan eats and fashion, music and words, gadgets and software, photography, design, DIY/maker/hacker culture, NYC, running/fitness, cyborg anthropology, et cetera.

    dp at danielpacker dot org