Academia

Tracking thesis writing progress

It’s gradually getting closer to the three year PhD deadline in which I intend to submit, meaning I’ve got two and a half months to not only finish up my experiments but write up my entire thesis. To help motivate myself to work on this huge document (and definitely not as a form of procrastination) I’ve started recording my writing progress and am publicly displaying the data here. The idea is that I won’t want people (family, supervisors, colleagues) to notice that I’m slacking.

Introduction to Python for Engineers

Today I gave a talk introducing Python to early stage researchers in my Department. It’s always hard deciding what material to include in an hour’s talk, particularly when the subject material is so vast. This wasn’t helped by the fact that in my department there is a large range of programming experience, from researchers with backgrounds in Computer Science to Electronic Engineers who are only comfortable with Matlab. I attempted to address both of these groups by introducing Python as a language in terms of its syntax, data structures and control flow, before discussing how you can emulate Matlab by using the SciPy stack.

Dplyr incompatibility with xtable

I’ve been working on another paper today and decided to update my previous xtable function (as described here) to use dplyr, as I want to fully get to grips with Hadley Wickham’s wonderful ecosystem of packages including dplyr (and its predecessor plyr), ggplot2 and tidyr (and its predecessor reshape2). I mentioned this before Christmas but have only got round to it now, which included a few hours of struggling with tidyr to make it do what I want!

Formatting reproducible tables for scientific research with Sweave

I’ve recently decided to start using Sweave for producing my publications since I already use R for the data analysis side and LaTeX for the markup, so it seems natural to combine them. In a nutshell, Sweave lets you embed R output directly into your documents, allowing for a more organised workflow. You mark a section as containing R code, then run your analyses with your output, be it in the form of text, a table, or a chart, formatted directly into LaTeX markup.

York Doctoral Symposium 2014

Last week on the 30th October the 7th annual York Doctoral Symposium took place. This is a 1 day Symposium run by post-graduate students from the Computer Science and Electronics departments at the University of York. It provides a fantastic opportunity for students to gain experience in writing papers or posters, giving presentations and network with other researchers in their field. Another key benefit of the symposium is that it gives experience in organizing and running a conference to the students who are on the organizing committee, a valuable skill to have for anyone pursuing an academic career.

Premature optimisation is the root of all evil...

I’ve found this saying to be particularly true these last couple of weeks. Having passed my confirmation viva I wanted to spend a bit of time cleaning up my code that has got rather bloated with all the recent additions to it. Since I’ve never been formally taught OO programming I decided to brush up on this as well. I bought the “Gang of Four” classic Design Patterns book and decided to implement as much as I could of it in my program.

Second year poster competition

As part of the PhD programme we have to produce a poster in our second year which are then judged by the head of the research groups. It was the first poster I’ve done so wasn’t too sure about things such as layout, font size etc… but it turned out pretty well in the end, and even won the second prize so was very happy with that! It’s a brief summary of some of the work I’ve been doing over the last 18 months, I decided to focus on the Parkinson’s Disease research as that’s more interesting to the layman rather than my current ensemble work.