Monday, July 11, 2016

Figuring out which adapters to trim in Illumina data

Often times it's difficult to know what adapter sequences should be trimmed from Illumina data. This can occur if you download public data, for example from SRA or if you send samples for sequencing to a company that doesn't communicate with you very well (not that I have any experience with that...).

Previously it's been a bit of a a struggle for me to figure out which adapters to trim when processing Illumina high-throughput sequencing data. With a little bit of time, and some thought about how Illumina sequencing works, adapters can be identified and removed even if we don't know beforehand what the sequences are.


Read on to see how I figured out the adapter sequences in my most recent RNAseq analysis.

Monday, July 4, 2016

Making a stoichiometric model of peppermint trichomes


Someday this work will be published with a more coherent and organized version of these methods. But maybe in the meantime, this will be useful to someone. Here's (more or less) my lab notebook for how I generated a stoichiometric model of metabolism in peppermint glandular trichomes.


Conversion of the Arabidopsis model by Arnold and Nikoloski, 2014, into a model using MetaCyc metabolite names

I think the stoichiometric model of Arabidopsis thaliana by Anne Arnold and Zoran Nikoloski (2014) is a great model. However, they use idiosyncratic and non-standardized metabolite names. I translated these names into MetaCyc compatible names. Here I describe and link to the conversion. The whole conversion table is available on Google Sheets, here.


Future perspectives for stoichiometric modeling

These are a set of notes I wrote for a specific proposed stoichiometric modeling project. I've edited out some of the details because someone is actually working on this project, but I think what remains is still worth reading.

Things you need to know for writing a thesis or dissertation in Microsoft Word: Styles, Style breaks, Tables of Contents, and more!

In writing my dissertation, I've had to become more familiar with some of the more advanced features of Microsoft Word (I know, I know, I should be using LaTeX, but that's just not what people in my field use...). Here are a few of the most critical tricks I've learned. I hope this is helpful to other people as they write long documents like theses and dissertations. The screenshots here are from Word 2016, but all of these things are very similar on Word 2010 and 2013.


Sunday, July 3, 2016

Random discrete distributions (decks) in game development

Randomness plays an important role in many games. Enemies appear randomly, or events occur at randomly spaced intervals. A relatively easy way to think of random events in a game is as a deck of note cards. The probability of a particular word being drawn is a function of the number of cards in the deck with that word on them, and the total number of cards in the deck.

This approach is called a discrete distribution.

In the case of circle the aardvark, I used a discrete distribution to determine whether an aardvark or an enemy spawned, and how long each character should remain on the screen before timing out and going away.

The game is written in Monkey X, but the code in this post is in Python.
You can find the Monkey X version here.


Read on for details

Tuesday, June 21, 2016

Can compassion ever be powerful enough to stop terrorists?

Our country and our world keep experiencing devastating and seemingly senseless acts of mass violence. Some of the violence is committed by people who are clearly mentally ill. But a shocking amount of mass violence is committed by rational people who know exactly what they are doing. My ideological heroes, like L.L. Zamenhof, Amon Hennacy, and Leo Tolstoy, were strong proponents of non-violence, even to the point of pacifism.

In my life as a middle class American (that is: incredibly wealthy compared to the world-wide norm), I've never really experienced the threat of violence, so perhaps I'm a little rosy-eyed and unrealistically idealistic. But it seems to me that our strongest weapon against violence is, and will always be, compassion.


Here's a poem that kind of addresses these issues. I wrote it after reading the article “Young Lives, Lost in the Fog of War” by Rod Nordland in the Sept. 15 2012 New York Times.

I'd be remiss if I didn't also credit the inspiration of the Flaming Lips, and their performance at the Oklahoma City Zoo, an Bart Budwig for a line I stole from one of his songs.