Pleuni: Hi Graham, when did you first learn to program?
Graham: I took one C++ class in my early twenties (at a community college, shortly after finishing my B.S.). After that, I didn’t do any programming at all until I started working in Scott’s lab* in 2013 for my Master’s. I chose Python primarily because I knew it was used for some bioinformatics research, and was more multi-purpose than R.
* Scott’s lab is Scott Roy’s group here at SF State.
Pleuni: What do you work on? Why is python useful for that?
Graham: My primary language for the last 6 years has been Python, which I’ve used to write all of the analyses I’ve done for my research. In my graduate work, I use comparative genomics to investigate various aspects of eukaryotic gene structure evolution, with a specific focus on a sub-group of spliceosomal introns. The longest single script I’ve ever written is ~6,000 lines long, and was the first big project I started during my graduate studies. Over the course of working in bioinformatics, I’ve built up a collection of Python scripts that I use very regularly in my work.
Over time, some things that I used to do in Python (largely file format manipulation, etc.) have been replaced by Bash, but otherwise, I still use Python fairly exclusively.
“Python is easier to pick up then other options”
Pleuni: Why did you pick Python?
Graham: I have found Python useful for a number of reasons. First and most pragmatically, the syntax is fairly straightforward and arguably less intimidating than some other languages, and I think that makes it easier to pick up than many other options. Second, it functions well as a “glue” language, which is essentially the role Perl used to occupy in previous decades. You can write Python code to perform statistical analyses, plot data, organize/manage files, and also to tie together existing software into more complicated pipelines.
Finally, I think that for students thinking about learning to code, Python offers the advantage that even if they don’t end up working in research science, learning Python is very likely to still be of some benefit. From what I understand this would be less true of, say, R—R is incredibly important and dominant in certain fields of academic research, but outside of those applications it is not as heavily used.
Pleuni: What do you work on in your PhD?
Graham: I use comparative genomics combined with next-generation sequencing to help to understand the evolution of different aspects of eukaryotic gene structure.
“I am studying a rare form of spliceosomal intron”
I am studying a rare form of spliceosomal intron which has undergone many instances of complete loss in many different eukaryotic genomes. By comparing the conservation of these introns across the eukaryotic tree, I can address questions related to their likely origins and dynamics within different genomic contexts.
Pleuni: Does this mean that you study introns and you compare their occurrence / their sequences / their locations in genomes of many different eukaryotic species to try and learn about their evolutionary history?
Graham: Yes!
Here you can see the code that he is working on. Many programmers share their code on Github. Graham on Github: github.com/glarue
Graham is a co-author on several published papers. He lives in Merced, CA, and has a 2-year old kid.
Link to paper: https://www.sciencedirect.com/science/article/pii/S0960982216315391
Being A Better Scientist 