Archive for December, 2014

Initial steps towards reproducible research

4 Dec 2014

In anticipation of next week’s Reproducible Science Hackathon at NESCent, I was thinking about Christie Bahlai’s post on “Baby steps for the open-curious.”

Moving from Ye Olde Standard Computational Science Practice to a fully reproducible workflow seems a monumental task, but partially reproducible is better than not-at-all reproducible, and it’d be good to give people some advice on how to get started – to encourage them to get started.

So, I spent some time today writing another of my minimal tutorials, on initial steps towards reproducible research.

It’s a bit rough, and it could really use some examples, but it helped me to get my thoughts together for the Hackathon and hopefully will be useful to people (and something to build upon).

The value of thesis intro/discussion

3 Dec 2014

Last week, Kelly Weinersmith tweeted:

Is any task a more monumental waste of time than writing an introduction and discussion for a dissertation where the chapters are published?

I think many (or most?) of my colleagues would agree with her. The research and the papers are the important things, and theses are hardly read. Why spend time writing chapters that won’t be read?

My response was:

Intro & disc of thesis get the student to think about the broader context of their work.

I’d like to expand on that just a bit.

In the old days, a PhD dissertation was more of a monograph. The new style is to have three or so papers (published or ready-to-submit) as chapters, sandwiched between introductory and discussion chapters. Those intro and discussion chapters are sometimes quite thin. I would prefer them to be more substantial.

The focus on papers is a good thing, as they will be easier to find and more widely read. But a thesis/dissertation is not just a research product, but also a vehicle to get a student to think more deeply and broadly.

The individual papers will include introductory and discussion sections, but journal articles tend to be aimed towards a relatively narrow and specialized audience. More substantive introductory and discussion chapters can help to make the work accessible to a broader audience. They also help to tie the separate papers together: what is the larger scientific context, and how do these pieces of work fit into that?

I don’t want students wasting time on “busy work,” and writing a thesis does seem like busy work. But I think a thesis deserves more than a ten-paragraph introduction. And the value of that introduction is not so much in demonstrating the student’s knowledge, but in being part of the development of that knowledge.