What Are Your Requirements When Examining A Bioinformatics Related Phd Thesis?

Question

[Steve Moss]

I had a read of this post by Mark Pallen recently, on what he discusses are his minimum requirements for examining a PhD thesis, with a particular focus on molecular bacteriology. It got me thinking about the requirements of different examiners in their respective fields of expertise.

I wondered what people here might have to add to this? I know it's a very general question and as such I'm not expecting a specific type of answer. I'm particularly interested in what you think one should be able to demonstrate as a minimum standard in your overarching area of expertise, although perhaps with a focus on bioinformatics, this being a bioinformatics forum after all.

My research relates to understanding the evolution of the genome with a particular focus on non-coding DNA and gene duplication, utilizing phylogenetic comparative methods and evolutionary bioinformatics approaches, applicable to the study of large-scale genomics data. Any comments relating to these areas would of course be most appreciated and helpful from my perspective. However, I am not asking that this be limited to just my particular field, as I would like to see if any consensus comments are made by those with experience in examining theses, that might assist people when producing a PhD thesis in general.

Perhaps this could become a reference post for those members considering a PhD in a bioinformatics related field, writing up their theses, or preparing for their viva's?

[Brad Chapman]

Steve, my best advice is to discuss this with your major professor and committee. By definition, your PhD work will be narrowly focused on a specific topic and they are the best ones to guide you. The graduate school experience is setup specifically to support this, so it's hard to beat using those resources. Additionally, those are the people you have to please to graduate so it's best to focus your energy on their thoughts instead of searching for more general objective criteria.

[Steve Moss]

Hi Brad, thanks for your comment! I know each PhD is very specific, which is why I was hoping people might be able to comment on what they require from PhD examination in their own fields. Not so much to help me, but to create awareness of where people fail to reach the required standard, in a similar way to Mark Pallen's post! I thought it would be useful to see if there is a consensus in any areas that people feel needs to be better addressed etc. Perhaps my question didn't quite put that forward? I'll update it to better reflect my thoughts!

[Steve Moss]

Hi Brad, thanks for your comment! I know each PhD is very specific, which is why I was hoping people might be able to comment on what they require from PhD examination in their own fields. Not so much to help me, but to create awareness of where people fail to reach the required standard in general, in a similar way to Mark Pallen's post! I thought it would be useful to see if there is a consensus in any areas that people feel needs to be better addressed etc. Perhaps my question didn't quite put that forward? I'll update it to better reflect my thoughts!

Answer 1

[Alastair Kerr]

The post you reference makes good points applicable to bioinformatics and non-bioinformatics PhD theses alike. I also strongly support Brads advice about speaking to and getting guidance from your school. Different countries do have different ideas in what constitutes a theses.

Your own research focus seems perfectly suited to the advice you linked. It appears to be an analysis based project and a thorough understanding of tools, techniques, background and scientific impact are just as important. I say to students I mentor that they need to know the computer programs they use just as well as a bench scientist should understand their wet work protocols. Science is science regardless of the technique.

One area I have seen that does cause confusion however is when the project is more focused in computer science. i.e. a key focus is application development. Here, in conjunction with the above points, researching and following up 'use cases' and good coding practices can be the norm. Complications arise if your mentors/committee only understands one aspect of your work. A CS thesis does look different from a biological one and adapting the best practice from both needs forward planning. Finding the right mentors (possibly out with your faculty/school) and having an open discussion with your supervisor/committee is critical.

[Steve Moss]

Many thanks for your answer Alastair. Most appreciated :)