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.

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.

Match The Mustelidae: a weasel themed memory game

In keeping with the recent trend of posting projects from my misspent youth, I present to you "Match the Mustelidae", which was the second "complete" game I ever made, right after Fasmo (which I will post later).

"Feeling Down" music video

This music video was my winter break project in 2010. The song was written and recorded by my brother Kyle. The animation was done with a Wacom pad, Gimp, and Blender. The animation style was inspired by the music video for the Moondoggies' Empress of the North (although I obviously don't have half the talent of Drew Christie)

On the pronunciation of "dehydrogenase", "hydrogenated", and "hydrogenation"

The words "dehydrogenase", "hydrogenated", and "hydrogenation" are typically (as far as I've noticed) pronounced with "drog" as the most emphasized syllable. That's how I used to pronounce it too. However, when TAing a biochemistry class taught by a rather ancient professor (Ron Brosemer, who has been teaching at WSU since 1963) I noticed that he pronounces these words with the emphasis the syllable "hy". So the "hydrogen" part of the word sounds exactly like it would if it were pronounced on its own.

At first that sounded weird to me, but now I think it actually makes a lot more sense than the typical pronunciation. It may be that Dr. Brosemer pronounces the words that way intentionally for pedagogical purposes. But I suspect that when he learned these words (presumably in the 1950's), his pronunciation was actually the typical way to pronounce them. There is no element pronounced "hydROGen", so it seems unlikely that the chemists who coined these derivative terms would have said it that way in their new terms. I think it is more likely that the modern common pronunciation arose in people (like me) who learned the terms before understanding their chemical significance.

Using Dr. Brosemer's pronunciation with these words, brings to mind their actual chemical meaning, a dehyrogenase is an enzyme that removes hydrogens from one of its substrates, and hydrogenated oils are oils which have had hydrogens added.

I've adopted Dr. Brosemer's pronunciation, and I think you should too.

Ammon Hennacy: Questions and Answers

This post is a continuation of the "Heroes in Their Own Words" theme that started with a translation of the Zamenhof's Declaration of Homaranism. Basically what I'm doing is finding and posting texts in which people who I consider to be heroes briefly describe their core beliefs. Ammon Hennacy was a self-described "Christian Anarchist". He spent 18 months in solitary confinement for resisting the draft during WWI, and was arrested over 30 times for picketing and tax evasion. Like Zamenhof, Hennacy lived a life that demonstrated a high degree of moral courage. He lived a life consistent with his ideals, and constantly propagandized against war even when it was obvious that his propaganda was incapable of effecting any major changes in the world. For this post I transcribed chapter 19 of Hennacy's autobiography, "The Book of Ammon" (pdf link). The book appears to be self-published and contains no copyright notice, and it is almost certain that Hennacy would not object to my transcribing and posting it. The chapter, called "Questions and Answers," is basically an FAQ of Hennacy's opinions in the period from 1950 to 1964. I don't agree with all of Hennacy's positions, but I think they are all well worth reading and contemplating. There's nothing in the world as valuable as passionate people speaking on topics they're passionate about. What follows are not my words, but those of Hennacy (there are some spelling mistakes in the original that I have corrected without note, hopefully without introducing too many new ones at the same time):

Poetry as a force of destruction

This is an essay about the limitations of poetry and the potential for the poetic process to destroy the information it intends to preserve. I think the ideas could also be applied to other forms of art. I wrote it in January of 2011, and revised it just now. I don't think this is by any means the last word on this subject (it's barely even the first word), and I welcome discussion.