Planning and planning and more planning

Alternate title: What has Kim been up to for a month and a half into her PhD?

Well, I've been doing my PhD for a month and a half now, and it's finally starting to become 'real', like, 'You really decided to stick to something for four years,' or 'You're really going to be able to pay rent this month without practicing the overdraft dance.' Money is quite nice, but having a purpose is nicer. Although, my exact purpose is still a little foggy...

See, despite applying to a PhD position that already had a funded project (the BINGO project, as I previously mentioned), as well as a description for my position (here), two paragraphs is not what you base four years of work on. This isn't a fully-prepared project for me to step into - that would be ridiculous and totally not what a PhD is supposed to be. No, I still have to do the reading and thinking and come up with a project proposal that both meets the needs of my research project yet is my own project, complete with goals and a timeline. What I need to complete in the first 5 or 6 months of my PhD, my friends, is a project proposal. And it will be a doozy.

One of many scribbled pages that make up my proposal process

The picture above is but one of my planning scribbles. I have a few more strewn across my desk, a notebook for more concise (and shareable) thoughts, a rough draft document on my computer, a task management system with to-do lists, AND a separate Evernote workbook for notes. It's intense. Too intense? I mean, in theory, I could just plop myself down in front of a computer and begin the process. Reading, synthesizing, creating, and then finally submitting a proposal. But in practice, it's much messier. And it ought to be.

In practice, my day-to-day existence in the office is far more varied. After biking to work, I get in around 10 am, and the first thing is coffee break (always 10.15) and most likely cake. The Dutch office thing about cake has previously been explained, so I won't go into further detail. After cake and coffee, I start by looking at my email (not much) and going through my RSS feeds. Because I currently have 69 subscriptions (quite happy with that number), this can take a while. I consider this essential, as most of my feeds are science, society, or scientific communication related, and it's a good way to start the day. The rest of the day is broken up by lunch and probably at least one meeting, sometimes a few - Tuesdays in particular are an onslaught of meetings and seminars - and one more coffee break in the afternoon. I head home at around 6.

See the disconnect between theory (steady work straight, instant product) and practice (interruptions, delay in output)? My supervisor would argue, and I agree, that it's a good thing. You have interaction with your colleagues, you learn about other projects, you help out others -- it's all good stuff that will pay off in the end, even if it's not immediately apparent. When it was clear that the deadlines I face are less strict than the ones I had placed on myself, I relaxed and settled into a work pace.


Alright, enough with the generalities, what am I actually working on?

I've read over ~30 articles in the last little bit, and have already expanded my knowledge quite a bit. I've done some GenBank assessments and research into my species and what sequences are available. I even have a map! My project proposal, the first draft anyway, is about halfway complete. However, it's missing two major components: the hypothesis and the methodology. It's one thing to say that I want to look at the population genomics and variation of three different biocontrol species (which is what I aim to do), it's another to say how and why I will do it.

When it comes down to it, there's a lot of how's to figure out. The most obvious (to those who use genetic sequencing) is what method and type of sequencing I will use - my proposal indicates second generation sequencing (SGS), but that's like saying my favourite kind of soda is the bottled kind. Reading articles can only get you so far, and there are some basics that I need to get a better handle on. To address this, I did two things: I took two MOOCs (Massive Open Online Course) in bioinformatics, and then signed up for a genomics course taught here at Wageningen UR.

The MOOCs (both on Coursera, one from University of Toronto and one from John Hopkins University). I chose these MOOCs over an IRL course because these were technically things I've already learned in my Masters course, but that was over two years ago and things were a bit unclear. So these were more refresher courses than new knowledge. That being said, the U of T course was a bit better quality than the JHU course but I recommend these courses and MOOCs in general to anyone - both of mine were free, and most MOOCs are free (in theory).

The genomics course taught here in Wageningen is from their Animal Breeding and Genomics Centre, and is taught by one of the collaborators on the BINGO project, so it's a pretty good fit for me. These concepts are a bit more foreign to me, so in-person learning will beneficial to me in this regard. The downside is that the course is every afternoon for six weeks (!). My progress will slow considerably. The course doesn't start until next week, so I have a few days to get things in order.

My current work space - no lab for me, yet

So there you have it. What I've been up to (work-wise) for the past month and a half! We'll see how often I can update and what I can and can't share. The latter is something that I get to address, sort of. It would surprise none of my friends back in Edmonton that I jumped at the chance to be one of the two PhD (here called Early Stage Researchers, ESRs) student representatives for our BINGO Network - there's a General Assembly and everything. I'm only a rep for 6 months: there are two reps, each with a year-long term that are staggered in 6 month pieces, so as the first one I opted for 6 months. I've done student representation before, and while I wanted my fellow ESRs to have the opportunity, I figured that I could use my own experience with the University of Alberta Students' Union to make sure that the structure is set up for others to take over. [If you listen closely, you can here a certain friend of mine yelling "NEEEEEEERD!" in the background] 

 A key area that I think needs to be addressed is a n agreement on social media for the whole project - I am really interested in opening up science, and want to be an ambassador for that in various ways, such as this blog, my Twitter, Facebook, guest posts, guest articles, etc. The reasons for sharing science via social media has had quite a bit of visibility over the past few years (here, here, and here), but has also had tales of woe. What I need is a fair and open policy to inform and back up what I can put out there. I want us all to be able to be fabulous science communicators, and I think a touchstone like an agreement or a policy would be helpful. [the last bit of the "-EEEERD!" is still echoing, isn't it...]

Collection O' Links
BINGO: Breeding Invertebrates for Next Generation BioControl
My project, RP1: Population Genomics of Natural Enemies
Stuff Dutch People Like, No. 18: Bring Your Own Cake
Coursera, Bioinformatic Methods I from University of Toronto
Coursera, Introduction to Genomic Technologies from John Hopkins University
Times Higher Education: Social media key to getting ahead, PhD students hear, by Holly Else
Medium: In defence of the love of science, by Signe Dean
The Sociological Imagination: 40 reasons why you should blog about your research
The Conversation: Talking about our work is important but it canland researchers in trouble, by Neil Levy and Francesca Minerva


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