Hugomatic

For the last few months,  I’ve had the great pleasure to work in a chemistry lab at McGill university alongside highly skilled and motivated scientists. I am not a chemist, so my job was simple: re engineer a molecular simulation program and make it run faster than the original using GPUs instead of CPUs as processing units. One of the great haha moments came when my collegue Ata and I managed to move our first molecule inside a protein using the conjugate gradient minimization method. At the time, I was only inspecting decreasing energy numbers dumped on a black terminal, but I used Pymol (an Open Source molecular visualization program) to create the above movie.

What is shown here is a graphical model of the Herpes Simplex Virus Type 1 Thymidine Kinase Interacting With (North)-Methanocarba- Thymidine.  The kinase is a large protein present in the body (shown as gray dots representing atom positions, and gray lines representing bonds), and the colorful molecule is the “cure”. The movements are rather small and jerky: they are the result of successively applying movements on each colored atom in the direction of the forces computed by our software.

But my adventures in Bio computing are coming to an end: I am taking my GPU skills to new adventures as of next month.

stay tuned…

http://en.wikipedia.org/wiki/Conjugate_gradient_method
http://en.wikipedia.org/wiki/Force_field_(chemistry)
http://en.wikipedia.org/wiki/Molecular_modeling_on_GPU

A while back (in 2007) I needed to make engravings on my mill so I wrote a little python plugin for a vector drawing program (Inkscape). When I got it working I thought it could be useful do I wrote a quick tutorial on EMC’s wiki along with the code. I abandoned the tutorial (and Inskscape plugin development) and wrote a standalone SVG to gcode app.

Three years later I find that there have been 31 revisions to the tutorial, others have run with the code, fixed it, enhanced it (its way, way, way better now), GPL’d it, and published it in its own repository http://bitbucket.org/jst/inkscape-gcode/

http://wiki.linuxcnc.org/uploads/inkscapegcodeeffect.png
This is magic, and it feels very good

My only regret is that I did not pay attention to this earlier, because I’m sure I would have met some very interesting people.

This is my first post. Check out my about video, created with the help of Noe and Shariff from Parafilms