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[Top 5 Things I Wish I Knew When I Started a PhD]

Added on 06/05/2015

In a short moment self-reflection, I made a list of the five most important things that doing research with a lot of data has taught me. And I learned the hard way - wasting a lot of time and energy re-doing things instead of being smart about it at the beginning. Note to self: I should read this once a year or so.

1. Take good notes while reading literature

Annotated PDFThere is nothing more annoying than having an excellent set of results to present, but finding it hard to go back to the motivation of the project and writing about why the results were produced. I find it really important to take notes at the beginning of a project, even if I am not sure if they will be relevant when my results are done.

I save a few notes at the top of each PDF I read and I also save relevant referenced sentences in a separate file. Sometimes it’s even just interesting ideas of other authors that I agree or disagree with.

Since experimentation work usually takes months to produce anything, having those background notes to fall back on is a big help when I want to get a paper ready or when I want to quickly scan through the papers I read. It is also great to read my notes from time to time while I am doing experiments, so that I don’t loose sight of the ‘big picture’.

2. Make scripts. As many as possible.

A bash script exampleAutomation of experiments in form of bash scripts is something that we all kind of know about but often don’t bother to do. However, I find that scripts that can set up and run simulations are very helpful in the long run and especially when I come back to re-running experiments I have forgotten details of.

Making bash scripts takes time though, which is why I didn’t do it at first. It didn’t seem that important. Then I had to change some simulation parameters and re-run everything. Again and again. Now, I simply invest the necessary time at the beginning, which makes me much more comfortable and ready to re-run anything I need to. And when I say script everything I mean everything - from automating the way input files are set up, executable files are run, results are sorted, sometimes even the way I move between directories during experimentation.

3. Take good notes of the experiments performed

Experiment notesI use simulations instead of running real-world experiments because I can do tens of runs in a matter of minutes. Simulations are especially useful for experimenting with parameters. Vary this parameter, vary that. It’s all perfectly clear while I am doing it.

I used to sort my results with different parameters into folders and name the folders with abbreviations of parameter names and values. Until I had a big experiment that lasted for about half a year and then wanted to come back to it in a year. I understood nothing.

Now, I try to take very detailed notes of what experiments I am running and why. I note down what worked and what didn’t and why I decided to go with a particular set of parameters. Even if I delete data because it doesn’t produce anything useful, I note that down so that I don’t wander down that particular avenue in the future. Most importantly, I avoid abbreviations. Yes, my folder names are usually over 100 characters long, but at least I understand exactly what they mean.

4. Refactor, inherit, comment

Code with commentsGood code means well commented code with a minimum amount of lines to do the job asked. It’s generally known that making your code readable is a must if you ever want to come back to your experiments. In Object Oriented Programming, this also includes subclassing rather than using If statements when a particular algorithm gets too complicated.

Comments are at least as important as the structure of the code itself. For example, I find it a good practise to describe important variables when they are declared. Or to explain why a function (and especially a mathematical function that computes a result from variables) does that it does.

5. Make production of final figures as painless as possible

Image directory setupAfter a paper is submitted, it usually comes back from peer review with a number of requested changes. But the peer review process can take months. After so long, I often find it hard to figure out how exactly I produced particular figures from my data when I need to change them, especially as I usually have a lot of data and a lot of figures produced during analysis.

To minimise the time I need to reproduce the figures that appear in the paper, I now do two things: 1. Produce figures with a script (I use python) and setup some way of quickly producing just the figures for the paper. E.g. setting up a global variable in the python script, that if set to true will call the relevant functions, is a good idea. 2. Either output those important figures in a separate folder, or make aliases (that’s ‘shortcuts’, Windows users) to them in a separate folder. This saves a lot of time I previously used to spend going through image files when I looked for the updated images.

It’s not all just about what you do..

Everyone is different in the way they function. Just like many people, I was conditioned by a 9-5 job for a while (well more like 9-8 but ok). Doing a PhD has been a great opportunity to find the actual ideal time for me to work. Ideal working hours and work / rest balance are important. I guess, until you figure out the way your own brain works, you will work against yourself to some extent. Of course, if you work with others on a day-to-day basis, this becomes more difficult.

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The Hive Mind in Southampton

I had the privilege to present The Hive Mind, my new sci-fi puzzle game about insect-inspired construction with robots, at the University of Southampton Science and Engineering day last weekend. A lot of people came to play it and it was great to watch how they interacted with it - kids were often better at the game than their parents!

How will artificial life impact the future?

In 2013, I was a part of the TRUCE workshop at the Alife conference. The workshop brought together scientists and creative writers in order to create a cool book full of stories about A-life (artificial life) and artificial intelligence and about how it will impact our society in the future. As I am very interested in swarm robotics, sci-fi games and movies and generally how the future will look like when robots run around and are part of our everyday lives, I jumped at the opportunity to cooperate on the project.

The Awesomeness and the Curses of Gaming

I have recently watched 'Free to Play’, a documentary by Valve about professional e-sports that inspired this post. I really recommend everyone to watch it, I think that it expressed the struggles and emotions of gamers really well. Let me start by saying that I have been a gamer since my childhood and while I never want to do it professionally, as I have other goals in my life, I do spend on average an hour or two a day playing PC games...

Blizzard finally gone mad!

That's it - the artists and developers at Blizzard have finally gone mad to bring us Heores of the Storm - a game that puts all heroes from your favourite Blizzard games like Starcraft, Wacraft and Diablo together.


The main purpose of pyCreeper is to wrap tens of lines of python code, required to produce graphs that look good for a publication, into functions. It takes away your need to understand various quirks of matplotlib and gives you back ready-to-use and well-documented code.

Citations count fails to measure the impact of research

Academic career progress is often judged by so-called "h-index", that measures how much your research is being cited. I recently had a detailed look at what exactly the citations, specifically those reported by Google Scholar, amount to. Only a relatively small fraction of the reported citations corresponded to research being applied or reproduced in a meaningful way.