Perhaps this is somewhat off topic for the site (?), but I am currently writing up my PhD thesis which is part wet-lab and part bioinformatics. For the bioinformatics part, I have a section on “these are the tools I used and this is the analysis I got out”, and a section on “I wrote tool X and it does Y”.
But now i’m half-way through, I am not sure if my style is what a traditional bioinformatics PhD thesis should look like – particularly for the code I wrote. For example, am I supposed to talk about the algorithms used in detail, or is dumping the code in the supplementary section good enough – or does the code go in the results section? or maybe the methods?
Unfortunately for me, no one in my lab has written a Bioinformatics thesis in English. Therefore, I am asking very kindly if anyone would be happy sharing a link to their thesis here, which I can read over just to make sure i’m formatting things right :]
I always assumed each area of science had its own conventions on the thesis style, such as background/methods/results/conclusion for Biology, and perhaps Bioinformatics had a unique approach (for example, say, there is an unspoken rule that all code has to be benchmarked, for example), but after reading these comments I see it’s a lot more about writing in a style that best suits your particular thesis/project, rather than adhering to some rigid format.
In this case, i’ll write an e-mail to my thesis committee with the layout i’ve made so far and ask if they’d like to make any alterations before I write any more.