Using BioJava from R

Posted on April 10, 2015 by spencer

I’m a fan of literate programming. When I’m writing a paper, I typically use LaTeX to draft the paper, Java to generate the data, and R to create figures and do basic analysis. With Sweave (or the... Read More

ISMB 2012

Posted on July 20, 2012 by spencer

[caption id="attachment_336" align="alignright" width="225" caption="My badge for ISMB, showing admission to 3DSIG and BOSC, as well as ISMB membership and Open Access pride."]Read More

Topic Page update

Posted on April 30, 2012 by spencer

Two weeks ago our Wikipedia article on Circular permutation in proteins was featured in on Wikipedia’s mainpage as a “Did you know…” article: We were quickly replaced by the Ri... Read More

DNA font

Posted on February 10, 2012December 7, 2016 by spencer

I recently downloaded the Deja-Vu font family and discovered the open-source typography community. I thought it would be fun to try to make a font myself. Since much of my time is spent looking at bio... Read More

EVfold

Posted on January 10, 2012 by spencer

For our weekly journal club I talked about a new method for de novo protein folding called EVfold. [Slides] Details can be read in the paper (plus 15 page supporting text) Marks, D. S., Colwell, L. J.... Read More

PDB40

Posted on November 22, 2011 by spencer

I had a great time over Halloween at PDB40 at Cold Springs Harbor Laboratory, celebrating 40 years of protein structure. I especially like the talks from older structural biologist about the history o... Read More

Protein of the Day: GluCl

Posted on November 22, 2011 by spencer

I mostly post pretty proteins to twitter, but this one deserves more than one image. It’s a membrane pore protein called glutamate-gated chloride channel (GluCl). One of my students pointed it o... Read More

ISMB

Posted on July 22, 2011 by spencer

I had a great time attending 3DSIG and ISMB/ECCB in Vienna. The quality of the talks was very high and it was fun to meet so many other computational biologists. It is nice to finally put faces and pe... Read More

Mass Spectrometry Review of PTMs

Posted on June 8, 2010 by spencer

I’ve been taking CHEM 283 with Dr. Majid Ghassemian. It’s a practical lab course on mass spectrometry. For the final, we had to analyze a sample of alpha-casein (the main protein in cow mi... Read More

IL-1 Principle Motions

Posted on May 26, 2010 by spencer

For my rotation with Pat Jennings and José Onuchic I’ve been analyzing simulations of the IL-1 complex. I made up this page to display some of the movies I made of principle motions in IL-1R bo... Read More

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