Tuesday, 6 October 2015

Two years in: funding and data analysis

I'm two years into my PhD, which started officially on October the 1st 2013. This time last year, I had completed the following:

Completed my proposal and seminar
Collected female specimens from throughout NZ
Been handed some males from the public, and pinpointed good places to set pitfall traps
2 conferences with presentations
Begun sequencing for phylogeny
Found someone to help me with genetic and ecology fieldwork early next year.

I was a bit sad that I hadn't completed my objectives, and that real life got in the way of me devising my perfect routine. Over the past year, I got used to this. Everything takes longer than I think, and my initial objectives were rather unrealistic. Money, friends, and hobbies are all things that get in the way of doing my PhD, but they are also things that keep me sane, which is quite important. But instead of trying to cut them out of my life, which I have been trying to do but failing miserably, I have decided to live with them and take them into consideration when planning things. That has been much kinder to my blood pressure. Every day, I prioritise my PhD above everything else, but after I have done a bit of work I can do the other things that are screaming for my attention. I'm on track, I think, so it seems to be working. I have, however, become really bad at time management and answering my emails, because I have periods during the day when I want to work on my PhD and the rest of the world be damned. Plus I have discovered that one can "flag" one's emails to prioritise dealing with them. I can do the flagging part fine; it's the dealing with them that I usually forget.

My project went over its funding allocation for this year, which has meant that I had to stop lab work. It was good in a way, because I needed to stop anyway. It was getting to the point where I was trying crazy and superstitious ways to squeeze sequences out of extracts that probably can be sequenced using some method somewhere, but weren't worth trying every possible combination of every parameter and ingredient. After completing my last 96 sequencing attempts (as usual, most didn't work), I helped out on a field trip with some undergrads. While out there, we caught some male trapdoor spiders which would be really good to sequence. I still have them. I really hope I get enough money to sequence them before October next year. They are from an island and would be a really interesting piece to add to the puzzle. I completed my environmental data collection too (I think). So the only data I have left to collect is morphological.

Now I am doing DNA data analysis, which involves downloading programs which don't work, and trying to get them to work. I just cracked one yesterday, and went to use one that I have used since my honours project and know really well, but it needs downloading again, and it won't install, and it requires Java, and Java won't install. This used to really stress me out but now I feel weirdly zen about it all because it's familiar. The feeling when something finally works is incredible. I think when this PhD is over I'd like to write a book on basic molecular techniques and analysis for people like me. I get this feeling that everyone instinctively knows how to work these programs except for me, and then someone comes up to me and asks how to do something basic and I realise it isn't just me.

All I have to do is phylogenetic and niche modelling data analysis, then finish my thesis. A year's work, easily, hopefully?

Anyway, here's to the next and final year. Cheers!

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