So what exactly do you do? (a day in front of a computer)

From Phdcomics

Ever so often when I am asked about what exactly I am doing in my Phd, I always think for quite some time as if I had no idea. I start to notice this behaviour increasing popular among my peers as well when they get given the same question. This is not because we don’t know what we are doing, but rather we do not know how to characterise ourselves.

I am currently enrolled as a Phd student in bioinformatics, and this is what I do in a typical day:

What I do (grant version)

Understanding the evolutionary forces that shape the genomic variations between and within different yeast species. A day of work would involve categorising and analysing polymorphism/divergence and estimate parameters that would explain the effectiveness of different evolutionary forces acting on the DNA level.

What I really do:

1. I code and make tables. I have a DNA sequence alignment since 2005. I have been trying to extract everything from the alignment for 2 years and counting. Whatever you can think of with a DNA alignment, I have done it all (yes, been there, done that). This either involves making the alignment into a SNP dataset, feed into some program someone had published and hope the results come out fine. Or the program no longer works/does not suit slightly/no longer being maintained, and you write yourself one. (Current achievement: writing almost every function of DNAsp with missing data in Perl) In the end you have a big big big table. (time spent: 5 minutes ~ days)
2. I make graphs. big big big table -> human readable graphs. Depending on how much money your boss have greyscaling the graph can be a real…. (time spent: 5 minutes ~ hours if publishing deadline approaching )
3. I read papers. This will take ages. Papers with good results often mean you have to dig the real methods from supplementary materials. Reading the papers as if you are the reviewer. (time spent: depending on the level of kindness of the authors)
4. I interpret the results. This is what/why you work hard for. (time spent: 1 minute)
5. I re-run everything I have done in the last 2 years, in 30 minutes. Results are fascinating, and you have to confirm it. Sure! Re run everything you have done before, and realising your Phd is in effect, 30 minutes of work if someone has published a good program to calculate everything (time spent: 30 minutes and days questioning yourself)
6. I write. Results are fine and confirmed. Now I need to make sure everyone (aka supervisor) understand it. (time spent: depends)
7. I moan. A problem people can realise from the list above is that I have not done anything novel. The results are novel, but all the methods are old. Is that a PhD? I do know for a fact that I am not qualified for most jobs currently advertising, something like the desired candidates would need to design novel statistical tests. (time spent: forever)

(tea breaks/supervior meetings/seminars/daydreaming/blog reading not included)

This is my typical day of work, and I would call myself a genomic data analyst with experiences of dealing large genome datasets and good statistical knowledge and very quick coding hands and a very fundamental understanding of biochemistry/molecular biology and know a bit of everything (note: this is not a self promotion post). This is what we do: we are biologists that have a lot of and in our roles.

And personally I have the integrity to make sure my paper is not just another genome analysis paper that publish summary statistics and mention future directions. I make sure other scientists can repeat my analysis in 30 minutes with my alignment or any well established alignment and see the significance of it.

So what exactly do you do?