Question: Bioinformatic PhD Thesis
2
gravatar for John
3.0 years ago by
John12k
Germany
John12k wrote:

Hello all,

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 :]

Thank you very much!

phd thesis • 1.9k views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by John12k
2

Ask your thesis committee and your supervisor, at least one of them should know. If nobody can help you, my advice would be to write a biological story. Computational approaches should be treated like other methods as they were the means to reach some biological conclusion just like wet lab experiments. See genomax2's comment.

ADD REPLYlink written 3.0 years ago by Jean-Karim Heriche19k
1

The appropriate style is for your advisor and committee to decide. We can't tell you what they will approve. Google/Scholar might have examples of course.

ADD REPLYlink written 3.0 years ago by karl.stamm3.5k
1

Fidel will have written his in English, swing by the office tomorrow and ask him for advice. Having said that, as Karl said, the only thing that matters is that your committee is happy. Aside from that nothing else matters.

ADD REPLYlink written 3.0 years ago by Devon Ryan90k
2

In a practical sense that may be true .. yes @John wants to graduate but including relevant information in the body of the thesis will make the tome comprehensive [Not sure if anyone else besides @John will read this after he graduates but the information will be there for posterity :-)].

@John: Sounds like your thesis is more biology (and relatively less bioinformatics, otherwise you would not be asking this question). How about describing the way your algorithm works (and why you designed it that way) in the methods section for of the thesis in plain English so a biologist can understand the flow of thought/work. Then put the code in supplemental materials (I assume the thesis will be in electronic format so the code can be accessible) to make the package complete.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by genomax68k
1

I think you should use scientific words whether your work is related to experimental or computational.

ADD REPLYlink written 3.0 years ago by sakshisingh.bioinfo30
2
gravatar for John
3.0 years ago by
John12k
Germany
John12k wrote:

Thank you all for your helpful replies!

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.

Thank you all so much :)

ADD COMMENTlink written 3.0 years ago by John12k
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