Thursday, October 13, 2016

rendering zdock server results using python and UCSF Chimera

I was interested in learning where the protein-protein interaction sites were on a particular protein (the receptor). I had pdb files for that protein, and for three proteins that it is known to bind to (the ligands). There are specific amino-acids of interest on the receptor protein, where there is variability among different species. For every combination of receptor and ligand, I want to perform a prediction of where the proteins interact, and then generate an image where the variable amino-acids are highlighted.

Gratefulness and Compassion meditation

Meditation is a way to slow down and appreciate life. For me, it is a way to relax, and prepare for the day, and to fight back against negative thoughts and attitudes that sometimes accumulate in my mind.

There's no one right way to meditate. You can try to empty your mind. You can focus intently on your breath, or on some mantra, or on different parts of your body. You can listen carefully and try to concentrate on perceiving your surroundings. The only rules are to be calm and to be positive. Meditation can sometimes veer into or negative thinking, or rumination: thinking about how other people owe you something, or how you've been mistreated or disrespected, or how you're somehow in an unfixable situation (you're not). Take care that your meditation does not become rumination.

I like to try out different kinds of meditation. Some I read about, some I invent on my own. I recently explained how I think that gratefulness and compassion are the two most important emotions. The rest of this post explains Gratefulness and Compassion Meditation, which is a way to cultivate those two emotions through practice.

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.

A separate, complementary but more useful, guide for the same thing, including all of the code, can be found on in a bitbucket repository here

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.