Blog Archives

Back to school special

Funny-Back-to-School-Sign

Unimatrix-0 High School has really excellent attendance and discipline statistics

So, another academic year is about to hove into view over the horizon, and what better time to take stock of your situation, make sure your gear is fit for purpose, and think about levelling-up your geek skills to cope with the rigours of the next year of academic life. If you need any hardware, Engadget’s Back to School review guides are a great place to start, and have reviews of all kinds of things from smartphones to gaming systems, all arranged helpfully in several price categories.

If you really want to be ahead of the game this year though, you’ll need to put in a bit of extra time and effort, and learn some new skills. Here are my recommendations for what computing skills psychology students should be learning, for each year of a standard UK BSc in Psychology.*

If you’re starting your 1st year…

A big part of the first year is about learning basic skills like academic writing, synthesising information, referencing etc. Take a look at my computer skills checklist for psychology students and see how you measure up. Then, the first thing you need to do, on day one, is start using a reference manager. This is an application that will help you organise journal articles and other important sources for your whole degree, and will even do your essay referencing for you. I like Mendeley, but Zotero is really good as well. Both are totally free. Download one of them right now. This is honestly the best bit of advice I can possibly give to any student. Do it. I just can’t emphasise this enough. Really. OK. Moving on.

Next you need to register for a Google account, if you don’t have one already. Here’s why. Then use your new Google username to sign up for Feedly and start following some psychology and neuroscience blogs. Here and here are some good lists to get you started. If you’re a real social-media fiend, sign up for Twitter and start following some of these people.

You may want to use the 5GB of free storage you get with Google Drive as a cloud back-up space for important documents, or you may want to sign up for a Dropbox account as well. Use one or the other, or preferably both, because none of your data is safe. Ever.

You’ll want to start getting to know how to use online literature databases. Google Scholar is a good start, but you’ll also need to get familiar with PubMed, PsycInfo and Web of Knowledge too.

If you’re really keen and want to learn some general skills that will likely help you out in the future, learn how to create a website with WordPress or Github Pages.  Or maybe download Gimp and get busy with learning some picture editing.

If you’re starting your 2nd year…

This is when things get more serious and you probably can’t expect to turn up to tutorials with an epically massive hangover and still understand everything that’s going on. Similarly, you need to step it up a level with the geekery as well.

You probably learned some SPSS in your statistics course in the first year. That’s fine, but you probably don’t have a licence that allows you to play with it on your own computer. PSPP is the answer – it’s a free application that’s made to look and work just like SPSS – it even runs SPSS syntax code. Awesomes. Speaking of which, if you’re not using the syntax capabilities of SPSS and doing it all through the GUI, you’re doing it wrong. 

If you really want to impress, you’ll start using R for your lab reports. The seriously hardcore will just use the base R package, but don’t feel bad if you want to use R-Commander or Deducer to make life a bit easier. Start with the tutorials here.

If you’re starting your 3rd year…

This is the year when you’ll probably have to do either a dissertation, a research project, or maybe both. If you’re not using a reference manager already, trying to do a dissertation without one is utter lunacy – start now.

For your research project, try and do as much of it as you can yourself. If you’re doing some kind of survey project, think about doing it online using Google Forms, or LimeSurvey. If you’re doing a computer-based task, then try and program it yourself using PsychoPy. Nothing will impress your project supervisor more than if you volunteer to do the task/survey set-up yourself. Then of course you can analyse the data using the mad statz skillz you learned in your second year. Make some pretty looking figures for your final report using  the free, open-source Veusz.

Learning this stuff might all sound like a lot to ask when you also have essays to write, tutorials to prepare for, and parties to attend. However, all these things are really valuable CV-boosting skills which might come to be invaluable after you graduate. If you want to continue studying at Masters or PhD level, potential supervisors will be looking for applicants with these kinds of skills, and solid computer knowledge can also help to distinguish you from all the other psychology graduates when applying for ‘normal’ jobs too. It really is the best thing you can learn, aside from your course material, naturally.

Have I missed anything important? Let me know in the comments!

Good luck!

* I realise US colleges and other countries have a different structure, but I think these recommendations will still broadly apply.

Psychology experiments enter the post-PC era: OpenSesame now runs on Android

smartphones-picard-uses-androidI’ve mentioned OpenSesame briefly on here before, but for those of you who weren’t keeping up, it’s a pretty awesome, free psychology experiment-developing application, built using the Python programming language, and it has a lot in common with PsychoPy (which is also awesome).

The recently-released new version of OpenSesame has just taken an important step, in that it now supports the Android mobile operating system, meaning that it can run natively on Android tablets and smartphones. As far as I’m aware, this is the first time that a psychology-experimental application has been compiled (and released to the masses) for a mobile OS.

This is cool for lots of reasons. It’s an interesting technical achievement; Android is a very different implementation to a desktop OS, being focused heavily on touch interfaces. Such interfaces are now ubiquitous, and are much more accessible, in the sense that people who may struggle with a traditional mouse/keyboard can use them relatively easily. Running psychology experiments on touch-tablets may enable the study of populations (e.g., the very young, very old, or various patient groups) that would be very difficult with a more ‘traditional’ system. Similarly, conducting ‘field’ studies might be much more effective; I can imagine handing a participant a tablet for them to complete some kind of task in the street, or in a shopping mall, for instance. Also, it may open up the possibility of using the variety of sensors in modern mobile devices (light, proximity, accelerometers, magnetometers) in interesting and creative ways. Finally, the hardware is relatively cheap, and (of course) portable.

I’m itching to try this out, but unfortunately don’t have an Android tablet. I love my iPad mini for lots of reasons, but the more restricted nature of Apple’s OS means that it’s unlikely we’ll see a similar system on iOS anytime soon.

So, very exciting times. Here’s a brief demo video of OpenSesame running on a Google Nexus 7 tablet (in the demo the tablet is actually running a version of Ubuntu Linux, but with the new version of OpenSesame it shouldn’t be necessary to replace the Android OS). Let me know in the comments if you have any experience with tablet-experiments, or if you can think of any other creative ways they could be used.

TTFN.

 

Links page update

Just posted a fairly major update to my links page, including new sections on Neuropsychological/Cognitive testing, Neuromarketing/research businesses, and Academic conferences and organisations, plus lots of other links added to the existing sections, and occasional sprinkles of extra-bonus-added sarcasm throughout. Yay! Have fun people.

Website of the week: Cogsci.nl. OpenSesame, illusions, online experiments, and more.

A quick post to point you towards a great website with a lot of really cool content (if you’re into that kind of thing, which if you’re reading this blog, then I assume you probably are… anyway, I digress; I apologise, it was my lab’s Christmas party last night and I’m in a somewhat rambling mood. Anyway, back to the point).

So, the website is called cogsci.nl, and is run by a post-doc at the University of Aix-Marseille called  Sebastiaan Mathôt. It’s notable in that it’s the homepage of OpenSesame –  a very nice-looking, Python-based graphical experiment builder that I’ve mentioned before on these very pages. There’s a lot of other cool stuff on the site though, including more software (featuring a really cool online tool for instantly creating Gabor patch stimuli), a list of links to stimulus sets, and a selection of really-cool optical illusions. Really worth spending 20 minutes of your time poking around a little and seeing what’s there.

I’ll leave you with a video of Sebastiaan demonstrating an experimental program, written in his OpenSesame system, running on a Google Nexus 7 Tablet (using Ubuntu linux as an OS). The future! It’s here!

New ‘Links’ page

Just a quick notification to say that I’ve just put up a ‘Links’ page, accessible from the top-level menu on this site, or by clicking here. There’s a couple of hundred categorised and (more or less) colour-coded links there, all more-or-less relevant to psychology and/or computing. Hope it’s useful to someone, because it took me bloody ages… ;o)

More to come on the links page as I find more stuff/get around to it.

TTFN.

How to pilot an experiment

I got a serious question for you: What the fuck are you doing? This is not shit for you to be messin’ with. Are you ready to hear something? I want you to see if this sounds familiar: any time you try a decent crime, you got fifty ways you’re gonna fuck up. If you think of twenty-five of them, then you’re a genius… and you ain’t no genius.
Body Heat (1981, Lawrence Kasdan)

To consult the statistician after an experiment is finished is often merely to ask him to conduct a post-mortem examination. He can perhaps say what the experiment died of.
R.A. Fisher (1938)

Don’t crash and burn your experiment.

Doing a pilot run of a new psychology experiment is vital. No matter how well you think you’ve designed and programmed your task, there are (almost) always things that you didn’t think of. Going ahead and spending a lot of time and effort collecting a set of data without running a proper pilot is (potentially) a recipe for disaster. Several times I’ve seen data-sets where there was some subtle issue with the data logging, or the counter-balancing, or something else, which meant that the results were, at best,  compromised, and at worst completely useless.

All of the resultant suffering, agony, and sobbing could have been avoided by running a pilot study in the right way. It’s not sufficient to run through the experimental program a couple of times; a comprehensive test of an experiment has to include a test of the analysis as well. This is particularly true of any experiment involving methods like fMRI/MEG/EEG where a poor design can lead to a data-set that’s essentially uninterpretable, or perhaps even un-analysable. You may think you’ve logged all the data variables you think you’ll need for the analysis, and your design is a work of art, but you can’t be absolutely sure unless you actually do a test of the analysis.

This might seem like over-kill, or a waste of effort, however, you’re going to have to design your analysis at some point anyway, so why not do it at the beginning? Analyse your pilot data in exactly the way you’re planning on analysing your main data, save the details (using SPSS syntax, R code, SPM batch jobs – or whatever you’re using) and when you have your ‘proper’ data set, all you’ll (in theory) have to do is plug it in to your existing analysis setup.

These are the steps I normally go through when getting a new experiment up and running. Not all will be appropriate for all experiments, your mileage may vary etc. etc.

1. Test the stimulus program. Run through it a couple of times yourself, and get a friend/colleague to do it once too, and ask for feedback. Make sure it looks like it’s doing what you think it should be doing.

2. Check the timing of the stimulus program. This is almost always essential for a fMRI experiment, but may not be desperately important for some kinds of behavioural studies. Run through it with a stopwatch (the stopwatch function on your ‘phone is probably accurate enough). If you’re doing any kind of experiment involving rapid presentation of stimuli (visual masking, RSVP paradigms) you’ll want to do some more extensive testing to make sure your stimuli are being presented in the way that you think – this might involve plugging a light-sensitive diode into an oscilloscope, sticking it to your monitor with a bit of blu-tack and measuring the waveforms produced by your stimuli. For fMRI experiments the timing is critical. Even though the Haemodynamic Response Function (HRF) is slow (and somewhat variable) you’re almost always fighting to pull enough signal out of the noise, so why introduce more? A cumulative error of only a few tens of milliseconds per trial can mean that your experiment is a few seconds out by the end of a 10 minute scan – this means that your model regressors will be way off – and your results will likely suck.*

3. Look at the behavioural data files. I don’t mean do the analysis (yet), I mean just look at the data. First make sure all the variables you want logged are actually there, then dump it into Excel and get busy with the sort function. For instance, if you have 40 trials and 20 stimuli (each presented twice) make sure that each one really is being presented twice, and not some of them once, and some of them three times; sorting by the stimulus ID should make it instantly clear what’s going on. Make sure the correct responses and any errors are being logged correctly. Make sure the counter-balancing is working correctly by sorting on appropriate variables.

4. Do the analysis. Really do it. You’re obviously not looking for any significant results from the data, you’re just trying to validate your analysis pipeline and make sure you have all the information you need to do the stats. For fMRI experiments – look at your design matrix to see that it makes sense and that you’re not getting warnings about non-orthogonality of the regressors from the software. For fMRI data using visual stimuli, you could look at some basic effects (i.e. all stimuli > baseline) to make sure you get activity in the visual cortex. Button-pushing responses should also be visible as activity in the motor cortex in a single subject too – these kinds of sanity checks can be a good indicator of data quality. If you really want to be punctilious, bang it through a quick ICA routine and see if you get a) component(s) that look stimulus-related, b) something that looks like the default-mode network, and c) any suspiciously nasty-looking noise components (a and b = good, c = bad, obviously).

5. After all that, the rest is easy. Collect your proper set of data, analyse it using the routines you developed in point 4. above, write it up, and then send it to Nature.

And that, ladeez and gennulmen, is how to do it. Doing a proper pilot can only save you time and stress in the long run, and you can go ahead with your experiment in the certain knowledge that you’ve done everything in your power to make sure your data is as good as it can possibly be. Of course, it still might be total and utter crap, but that’ll probably be your participants’ fault, not yours.

Happy piloting! TTFN.

*Making sure your responses are being logged with a reasonable level of accuracy is also pretty important for many experiments, although this is a little harder to objectively verify. Hopefully if you’re using some reasonably well-validated piece of software and decent response device you shouldn’t have too many problems.

More useful links… Open Sesame, the psychology of email, Inkscape, and others.

Another quickie post (it’s been ages since I’ve written anything substantive I know, bear with me just a little while longer…) with some links-of-interest for you.

First up is Open Sesame – this is an experiment-builder application with a nice graphical front-end, which also supports scripting in Python – nice. Looks like a possible alternative to PsychoPy with a fair few similar features. Also, it’s cross-platform, open-source and free – my three favourite things!

Next up is Inkscape – this is a free vector graphics editor (or drawing package), with similar features to Adobe Illustrator or Corel Draw. I tend to use Adobe Illustrator for a few specialised tasks, such as making posters for conferences, and this looks like a potentially really good free alternative.

Neuroimaging Made Easy is a blog I found a while ago that I’ve been meaning to share; it’s mostly a collection of tips and downloadable scripts to accomplish fairly specific tasks. They’re all pretty much optimised for Mac users (using AppleScript) and people who use BrainVoyager or FSL for their neuroimaging – SPM users are likely to be disappointed here (but they’re pretty used to that anyway, right?! Heh…). Really worth digging through the previous posts if you fall in the right segments of that Venn diagram though – I’ve been using a couple of their scripts for a while now.

Penultimately, I thought this recent article on Mind Hacks was really terrific – titled: “Psychological self-defence for the age of email”. It covers several relevant psychological principles and shows how they can be used to better cope with the onslaught of e-mail that many of us are often buried under.

Lastly, I hope you’ll pardon a modicum of self-promotion, but I recently did an interview over Skype with the lovely Ben Thomas of http://the-connectome.com/. Unfortunately the skype connection between London and Los Angeles was less than perfect which meant he couldn’t put it up as a podcast, but he heroically transcribed it instead – if you are so inclined, you can read it here.

TTFN.

Video tutorial on designing and running psychology experiments using PsychoPy

PsychoPy is something which I’ve been meaning to write something substantive on for a while. Briefly though, it’s a system for designing and running experiments, programmed in the Python language, with a nice GUI front-end to it. I’ve only flirted with it briefly, but the open-source and cross-platform nature of it makes it a very attractive package for programming experiments, in my opinion. If I was learning this stuff for the first time, it’s definitely the system I’d use.

The purpose of this post was just to publicise a YouTube video, put up by the creator of PsychoPy – Jon Peirce, of Nottingham University. The video is a great little starter-tutorial for PsychoPy and gently walks the viewer through creating a simple experiment – great stuff.

Happy experimenting! Here’s the vid:

Matlab for Psychologists – 3-day intensive course at the University of Nottingham

I’ve just come across a fantastic-looking 3-day course running at the University of Nottingham called ‘Matlab for Psychologists‘. The curriculum looks like it starts from the very basics at the beginning of the course, and works up to some fairly advanced material by the end of the three days. The summer course has just finished, but there’s another one due to run in September.

Without a doubt, if you’re a PhD student or post-doc at the beginning of your research career, learning Matlab is certainly one of the most useful things you could possibly learn. You can use it for… well… everything really, since it’s a true, general-purpose programming language, albeit wrapped up in a semi-friendly GUI. Presenting stimuli with the psychophysics toolbox is one really popular usage in psychology research, as is general statistical analysis and plotting, and of course analysing fMRI data with the mighty SPM. If I was a PhD student I’d be begging my supervisor and/or department for the £375 to pay for this course – it’s likely to be some of the best money you’ll ever spend on your education.

The course is run by Antonia Hamilton of Nottingham University, and she also has some really good Matlab resources on her website here.

One other thing – while googling ‘Matlab for Psychologists’ I also came across this book with the same title, which was just published a few months ago. Not a whole-hearted recommendation as I haven’t read it, but it looks like it might be worth checking out if you’re keen to give Matlab a try and can’t get to the course.

A review of social science research using Facebook

A quick-ish post just to point you towards a fascinating review published last month in Perspectives in Psychological Science: Wilson, Gosling and Graham (2012) A review of Facebook research in the social sciences. These authors review a set of 412 (!) studies that have been published, all since Facebook was launched in 2004. One of the striking figures in their review is this one, which highlights both the meteoric increase in Facebook users (currently over 800 million) and the parallel growth in research papers which have used Facebook as a means to gather data:

Figure 1 from Wilson, Gosling and Graham (2012). People like using Facebook, and researchers apparently *really* like people who like using Facebook.

The 412 research reports were divided into five broad-ish categories, in terms of their aims:

1. Who is using Facebook?
2. Why do people use Facebook?
3. How are people presenting themselves on Facebook?
4. How is Facebook affecting relationships among groups and individuals?
5. Why are people disclosing information on Facebook despite potential risks?

The authors suggest that, as well as just being a descriptive characterisation of the literature, these five central questions might serve as a common framework for future research in other online social networks, especially research which seeks to compare patterns of usage across two or more networks. Seems reasonable.

Also of interest (to me, anyway) is Appendix B which details the major data collection methods used by the studies, and also discusses some ethical considerations. It notes that some researchers have built custom applications for Facebook in order to collect data, but that these applications are not always successful in attracting a large user-base, i.e. some ‘go viral’ and some do not. This seems like an opportunity to do some interesting ‘meta’-research; a study of which research-driven applications are successful, and which aren’t!

Online social networks are an important part of many people’s social lives nowadays, and it seems unlikely that their influence has even come close to peaking yet; we can only expect that take-up and usage of these social tools will carry on increasing (and perhaps even accelerating) for some time. It’s good to see that social scientists have embraced these new ways that we all interact and are making serious efforts to describe and evaluate them.

TTFN.