Wednesday, February 18, 2015

I am who I am

The breadth of topics covered on this blog may strike some people as weird. Just in the past five days the posts have included, the personal (poetry), the professional (my lab notebook and code from work for an article published in a peer-reviewed scientific journal), and the silly (a video of myself shaving with a trowel). My justification for this is that the blog represents my interests, and I basically use it as a forum to make available anything I do that I think other people might find useful or entertaining. I don't magically turn into a different person when I walk into the laboratory, or when I come back home. I'm me all the time and, like Walt Whitman, I contain multitudes, and so does this blog, and that's just how I like it. And if you're only interested in one particular topic, then you can use the keyword labels to filter out the things you couldn't care less about..... yep.

My other shaver is a double-edged razor blade duct-taped to a trowel

Even though I only shave a few times a year, I consider myself somewhat of a shaving enthusiast. I've tried straight razors, and double edged razors, and electric razors, and whatever the heck you call the things Gillette is selling these days.

What I've learned is that you don't really need anything special to get a decent shave. All you really need is a really sharp blade mounted firmly on a handle (some quality shaving soap also really helps). To prove that point, I decided to cut my big beard off with a razor blade duct-taped to a trowel!  Read on for details (and a 7.5 minute video of the act itself).

Monday, February 16, 2015

Comparing data from open natural products chemical spectral databases

I recently wrote a review article called "Open-access metabolomics databases for natural product research: present capabilities and future potential", for the journal Frontiers in Bioengineering and Biotechnology, section Bioinformatics and Computational Biology (link).

Part of the review involved evaluating the contents of In this post, this post consists of the notes I took when generating those comparisons. The code I used is available from my Bitbucket account (I apologize for the poor organization and near-lack of documentation), some of the scripts depend on srj_chembiolib, and/or Pandas. InChI normalization relies on ChemAxon molconvert.

Factors to compare: how many unique compounds are present in the database, how many structures have the various kinds of associated analytical spectra, what compound classes are represented.

Friday, February 13, 2015

Valentine's Day poems

It's Valentine's Day! To celebrate, here are some "love poems" that I've written over the years. I'll start out with a serious one before quickly devolving into the absurd.