Category Archives: Technology

Find somewhere to publish with Jane – the Journal/Author Name Estimator

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If you’re trying to decide on a journal to submit your latest manuscript to, Jane – the Journal/Author Name Estimator, can point you in the right direction. This isn’t exactly breaking news, but it’s worth a reminder.

To use Jane, copy and paste your title and/or abstract into Jane into the text box and click “Find journals”. Using a similarity index with all Medline-indexed publications from the past 10 years, Jane will spit out a list journals worth considering. Alongside a confidence score, which summarises your text’s similarity to other manuscripts published in that journal, you’re also provided with an citation-based indication of that journal’s influence within the field.

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The other available searches are the “Find articles” and the “Find authors” search, the last of which I suspect I would use if I were an editor with no idea about whom to send an article to for review. As an author, it’s worth running abstracts through these searches too to make sure you don’t miss any references or authors you definitely ought to cite in your manuscript.

There’s more information on Jane from the Biosemantics Group here: http://biosemantics.org/jane/faq.php.

Using the Raspberry Pi to Run Cognitive Psychology Experiments

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English: Extract from Raspberry Pi board at Tr...
The Raspberry Pi (photo credit: Wikipedia)

A few months ago, I suggested that Raspberry Pis could be used as a barebones experiment presentation machine. Since then I have got my hands on one and tinkered a little, only to be reminded yet again that my inability to do anything much in both Linux and python is a bit of a problem.

Fortunately, others with more technological nous have been busy exploring the capabilities of the Pi, with some exciting findings. On the Cognitive Science Stack Exchange, user appositive asked “Is the Raspberry Pi capable of operating as a stimulus presentation system for experiments?” and followed up at the end of January with a great answer to their own question, including this paragraph:

The RPi does not support OpenGL. I approached this system with the idea of using a python environment to create and present experiments. There are two good options for this that I know of, opensesame and psychopy. Psychopy requires an OpenGL python backend (pyglet), so it won’t run on the Rpi. Opensesame gives you the option of using the same backend as PsychoPy uses but has other options, one of which does not rely on openGL (based on pygames). This ‘legacy’ backend works just fine. But the absence of openGL means that graphics rely solely on the 700 mHz CPU, which quickly gets overloaded with any sort of rapidly changing visual stimuli (ie. flowing gabors, video, etc.).

Because of the lack of OpenGL support on the Pi, Psychopy is out (for now) leaving OpenSesame as the best cog psych-focused python environment for experiment presentation. The current situation seems to be that the Pi is suboptimal for graphics-intensive experiments, though this may improve as hardware acceleration is incorporated to take advantage of the Pi’s beefy graphics hardware. As things stand though, experiments with words and basic picture stimuli should be fine. It’s just a case of getting hold of one and brushing up on python.

UPDATE via Comments (1/4/2013) - Sebastiaan Mathôt has has published some nice Raspberry Pi graphics benchmarking data, which are well worth a look if you’re interested.
http://www.cogsci.nl/blog/miscellaneous/216-running-psychological-experiments-on-a-raspberry-pi-with-opensesame

Codecademy Stories

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A couple of months ago, the folks at codecademy were nice enough to respond to a complimentary e-mail I’d sent them by writing something nice back about me and publishing it on their codecademy.com/stories page.

cadecademic

It was great to get this sort of coverage on a site I think is fantastic (despite the picture of me with a rather supercilious looking one-year old on my back). The only problem was that I didn’t have a working example of code available for them to link to. The JavaScript experiments I had previously coded had run their course, garnering approximately 200 participants each, and had been taken offline, leaving the lab experiment page with nothing for people to try their hand at.

That changed today.  I have a very simple new experiment for people to try their hand at, which can be accessed via the experiments (online) link on the right, or directly, here: http://www.st-andrews.ac.uk/~oclab/memorywords/.

I’m afraid it doesn’t quite do justice to the “neuroscientist discovers javascript” headline on the codecademy stories page, but it’s something.

Twitter and Conference Socials

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On Monday I gave a talk on how internet tools can be used to make the job of being an academic a little easier.  I had given a very short version of the talk to faculty in the department over a year ago, but this time I was given an hour in a forum for  early career researchers, PhD students and postdocs.  The subject of twitter, covered early on in the talk, aroused a lot of interest, probably because I got very animated about its benefits for those in the early stages of their careers.

To provide a little context for my enthusiasm, it probably helps to know a few things about me, about my situation, and about my recent experiences.

  1. I am an introvert.  Despite my best (and occasionally successful) efforts to project a different image, I do not find talking to people I don’t know very enjoyable.
  2. I am an early career cognitive neuroscientist keen to build my own research programme and develop links with other researchers.
  3. Last month I attended the Society for Neuroscience conference, at which I attended the best conference social I have ever attended.

Given the received wisdom that people in my position ought to be networking, I often drag myself kicking and screaming to conference socials. The result tends to be a lot of standing around on my own drinking beer, which gives me something to do, but which I could do much more comfortably with one or two people I know well.  The major problem at these events is not my nature, or my status as an early career researcher, but the fact that the people I have imagined myself talking to usually don’t know who I am.  Conversation is therefore awkward, one-sided and introductory.  Once the niceties have dried up, and the level of accumulated conversational silence edges into awkward territory I invariably finish my drink and bugger off to get another one, ending the misery for all involved.  This is probably a universal experience for those starting out in academia, though thankfully it is happening less and less to me as I build something of network of real friends who attend the same conferences as me.  But as a PhD student and postdoc, the experience was excruciating.

I had a totally different experience when I attended the SfN Banter tweetup*.  The event, organised by @doc_becca and @neuropolarbear, was a social for neuroscientists who use twitter and changed my view of conference socials.  They do not have to be endured, even by those doing PhDs and postdocs. They can be enjoyed.

I was excited about going and that excitement didn’t leave me feeling shortchanged by the time I left.  I spoke (actually spoke!) to everyone I wanted to speak to.  Moreover, I had good conversations with people to whom I was speaking for the first time. The reason is fairly obvious – twitter allowed us to build on a body of shared (or at least assumed) knowledge. I follow people, they follow me,  I reply to or retweet their tweets, they do the same – and this is all before we’ve introduced ourselves. When I finally meet someone with whom I have such a history of communication, introducing myself is the least awkward thing I can do. The barriers to conversation are removed**.

Sure, this pattern followed for most interactions at the tweetup because we were all there to do exactly that.  Would the experience be the same at the ‘fMRI social’? No.  But, I don’t think that matters.  If I could have had one of those conference social experience during my time as a PhD student, it would have given me an idea of what I might have to look forward to from conferences if I stuck at it.  Light at the end of the tunnel, a pot of gold at the end of the rainbow, a variable-ratio schedule-determined stimulation of the limbic system following an umpteenth lever press.

It will take a while (there’s no point joining in September 2013 and expecting great things at the SfN tweetup in San Diego), and it’s probably not the primary reason to join twitter (see  Dorothy Bishop’s blog and Tom Hartley’s blog for far more comprehensive discussions  of how and why you should join), but it’s another reason, and it’s one that could make you feel good about your role in academia.  It’s worth a shot.

 

* tw(itter) (m)eetup, see?

** What you do afterwards is up to you.  I still had some awkward interactions, but I think that’s probably down to me (see context point 1).

Web-based Cognitive Psychology Experiments

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This year, I decided to learn how to present cognitive psychology experiments online. Five months in, I’m happy with my progress.

Since the second-year of my PhD, when I spent a couple of weeks getting nowhere with Java, I have been keen to use the web to present experiments. What enabled me to move from thinking about it to doing it was Codecademy. I’ve previously blogged about how useful I found the codecademy website in getting me familiar with the syntax of Javascript, but at the time of writing that post, I was unsure of how a knowledge of the coding architecture alone (and certainly not coding aesthetic) would translate into a webpage presenting a functional cognitive psychology experiment. Thankfully I did have a barebones knowledge of basic HTML, much of which is now obsolete and deprecated, from which I was able to salvage snippets to combine with CSS (thanks to w3schools) to get something functional and not hideously ugly.

Syllable-counting in the Study Phase.
(click to be taken to the experiment)

Before I present the experiment I have spent the past few months working on, here are a few things I have learned from the experience so far.

1) In choosing Javascript over a medium like Flash, I hoped to maximise the number of devices on which the experiments would run. I think I made the right choice. Pressing response buttons with your finger on an iPad or an Android phone feels like a Human Factors triumph!

2) Javascript-driven user-interaction operates quite differently to user-interaction in languages like Matlab. Javascript is user-driven, which means you can’t have the browser start an event that waits for a response – the browser will crash. Instead, you must start an event that changes the state of the elements within the browser, such that should those elements be responded to, it will be as if the browser had waited for a response.

3) It is very quick and very easy to learn how to code functionally… if it works – it is generally functional. It is much more difficult to learn how to code both elegantly and functionally. I do not know how to code elegantly and I don’t think I ever will. (I’m not flippant about this either.  This is something I would really like to learn how to do).

4) Getting everything to look OK in different browsers is a pain. It wasn’t so much the Javascript as the newer snippets of HTML5 that I have struggled to get to work in every browser.

5) Web security is a subject on which I have very little knowledge.

6) Sending information from a browser to a server is a pain in the arse.

 

And finally, here is the experiment:

http://www.st-andrews.ac.uk/~oclab/memoryframingexpt/

It is a fairly straightforward recognition experiment, takes about 15 minutes to complete and should provide data for use in a larger project, so do feel free to take it as seriously as you want. As I have already mentioned, it works on an iPad, and I thoroughly recommend you give it a go this way if you have access to one.

Codecademic

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Points and badges

For the past week or so, I have been working my way through Codecademy’s JavaScript tutorials. I can’t recommend them highly enough.

As things stand, I have a full house of 480 points and 35 badges and, as the Codecademy creators would undoubtedly hope, I am rather satisfied with the JavaScript proficiency I have attained. ‘Attained’ is probably the wrong word to use though. Being a self-taught Matlab hacker, I have found most of my coding know-how has translated fairly well into Javascript. A few concepts (recursion in particular) have presented me with some difficulty, but the overall experience has been more like learning a new coding dialect  than a new language altogether. I haven’t attained a proficiency, so much as uncovered a hidden one.

Which brings me to why I sought out Codecademy in the first place (thanks to @m_wall for the twitter-solicited tip-off) – I am preparing to teach Psychology undergrads how to code. From 2012/2013 onwards, my academic life is going to be a little more ‘balanced’. As well as the research, admin and small-group teaching I currently enjoy, I’m also going to be doing some large-group teaching. Although I have plenty to say to undergraduates on cognitive neuroscience and cognitive psychology, I think giving them some coding skills will actually be much more useful to most. As my experience with Codecademy has recently reinforced to me, coding basics are the fundamental building-blocks of programming in any language. They will hold you in good stead whatever dialect you end up speaking to your computer in. What’s more, they will hold you in good stead whatever you end up doing, as long as it involves a computer: coding is the most versatile of transferable skills to be imparting to psychology graduates who (rightly) believe they are leaving university with the most versatile of degrees.

With all this in mind, one of Codecademy’s limitations is the difficulty with which its students can translate their new-found JavaScript skills into useful ‘stuff’ implemented outside the Codecademy editor. As Audrey Watters points out, there is barely any acknowledgement within the Codecademy tutorials that the goal of all of these points and badges is to encourage you to write interactive web contact in an IDE. Indeed, last night when I thought about how I would use JavaScript to administer online  memory experiments, I had to do a lot more reading. This could all be about to change though. If the latest Code Year class on HTML is anything to go by, the folks at Codecademy are mindful of this limitation, and are attempting to remedy it.

It’s just a shame that the html integration has come so late in the Code Year (yes, I say this with full awareness that we’re only on week 13).  If the HTML-Javascript confluence had come a little further upstream, I think there probably would have been a fledgling memory experiment linked to from this blogpost!

Raspberry Pi and the lab of the future

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Raspberry Pi schematic from http://www.raspberrypi.org

I think the Raspberry Pi is going to be fantastic, for reasons summed up very nicely by David McGloin - the availability of such a cheap and versatile barebones technology will kickstart a new generation of tinkerers and coders.

It’s worth mentioning that this kickstart wouldn’t just be limited to the newest generation currently going through their primary and secondary school educations. Should my hands-on experience of the device live up to my expectations (and the expectations of those who have bought all the units that went on sale this morning), I will be ordering a couple for each PhD student I take on. After all, what’s the point in using an expensive desktop computer running expensive software on an expensive OS to run simple psychology experiments that have hardly changed in the past 15 years? What’s the point when technology like the Raspberry PI is available for £22? Moreover, if you can get researchers to present experiments using a medium that has also helped them pick up some of the most desirable employment skills within and outwith academia, expertise with and practical experience in programming, then I think that’s a fairly compelling argument that it would be irresponsible not to.

But won’t I have missed a critical period in my students’ development from technology consumers into technology hackers?

No.

Every psychology student can and  should learn how to code (courtesy of Matt Wall), and it’s never too late.  I  learned to code properly in my twenties, during my postdoc. The reason it took me so long was that I had never needed to code in any serious goal-driven way before this time. Until the end of my PhD, Superlab and E-Prime had been perfectly passable vehicles by which I could present my experiments to participants.  My frustration with the attempts of these experiment presentation packages to make things ‘easy’, which ended up making things sub-optimal, led me to learn how to use the much ‘harder’ Matlab and Psychophysics Toolbox to present my experiments.  Most importantly, I was given license to immerse myself in the learning process by my boss. This is what I hope giving a PhD student a couple of Raspberry Pis will do, bypassing the tyranny of the GUI-driven experiment design package in the process.  Short-term pain, long-term gain.

In a few years, my behavioural testing lab-space could simply be a number of rooms equipped with HDMI monitors, keyboards and mice. Just before testing participants, students and postdocswill connect these peripherals to their own code-loaded Raspberry Pis, avoiding the annoyances of changed hardware settings, missing dongles and unre

liable network licenses. It could be brilliant, but whatever it is, it will be cheap.

Reading pdf documents on an iPad

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Can the iPad2, with its 132ppi 1024 x 768 screen, be used to comfortably read pdfs without the need to zoom and scroll about single pages?

That was a question that troubled me when I was splashing out for one earlier this year. To try to get a better idea of what a pdf viewed on only 800,000 pixels might look like was hard. Neither my attempt to I resize a pdf window to the correct number of pixels (too small) nor my attempt to screengrab  a pdf at a higher resolution and shrink it using GIMP (too fuzzy) were particularly informative. I just had to take plunge and see.

There’s enough wiggle-room (as you can see in the screenshots below) to suggest that there’s no definitive answer, I think the answer is probably yes. But, that’s only if you take advantage of some nifty capabilities of pdf-reading apps, Goodreader being the one I use, mostly thanks to its almost seamless Dropbox syncing capabilities.

Below is a screengrab of a standard, US letter-size, pdf, displayed unmodified on the iPad. The size, when the image is viewed inline with this text (and not in its own separate window), is approximately the same as it appears on the iPad (there is some loss of resolution which can be recovered if you click on the image and open it in its own window).

Click on the image to simulate holding the iPad close to your face whilst squinting.

The screengrab above demonstrates that virgin pdfs aren’t great to read. The main body of the text can be read at a push, but it’s certainly not comfortable.

Thankfully, the bulk of the discomfort can be relieved using Goodreader’s cropping function, which allows whitespace around pdfs to be cropped out (with different settings for odd and even pages, if required).  A cropped version of the above page looks like this:
A marked improvement which could be cropped further if you weren't too worried about losing the header information. Click on the image to see the screengrab with no loss of resolution.

The image above demonstrates that cropping can be used to get most value from the rather miserly screen resolution (the same on both the iPad and iPad2, though almost certainly not on the iPad3, when that’s released).

But, cropping doesn’t solve all tiny text traumas.  There are some circumstances, such as with particularly small text like the figure legend below, that necessitate a bit of zooming.

The figure legend is a little too small to read comfortably, even when the page is cropped.

I don’t mind zooming in to see a figure properly, but that’s probably a matter of personal taste.

If you’re used to using an iPhone4, with its ridiculous 326ppi retina display, then you’ll find reading pdfs on a current model iPad a bit of a step back. But, it’s passable and I certainly don’t mind doing it. It certainly beats printing, carrying and storing reams of paper.

Of Google+, Mechanical Turk and Academic Early-Adopters

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Having deleted my facebook account nearly two years ago, as I activated a Google+ account this week I was wary of repeating previous mistakes.  Back in 2009 I had decided that I wasn’t getting as much out of facebook as I was putting into it. Specifically, I was ashamed at the amount of my time it consumed, I was worried, not so much about my privacy, as the disregard of my right to it (even if I chose not to take it up), and I was anxious about expressing myself too freely lest I cause offence to my friends.  Google+ has lessened my anxiety with its subdivision of friends into circles, though, of course, its potential to cause me shame and worry over my time and privacy are just as real as they ever were with facebook.

With all this in mind, my early experiences of Google+ have been very positive. As I was hoping to, I have re-connected with some lovely friends who had remained on facebook and never ventured onto twitter. Perhaps most encouragingly though, it looks like Google+ might be able to reach beyond the social, and enrich my professional life too. The following exchange, which I started to try and learn more about the use of Amazon’s Mechanical Turk in psychological research, is the sort of thing that’s making me very excited about this possibility.

Full Google Plus conversation

The discussion went in to far more detail than I could have hoped, and for those who are interested, a text-searchable pdf of the exchange complete with clickable links is available here.  (Incidentally, the reason I have had to go to so much trouble to provide a link to the thread with jpgs and pdfs, as opposed to the sort of easy html permalinking offered by twitter, is down to Google’s as-yet imperfect post-hoc sharing system. Once I decided that the thread deserved a wider audience, the options available to me were a) to re-share my original post, without the comments, to anyone on the web, or b) to provide a permalink to the whole thread that was only accessible to those with whom I had originally shared my first post. An option to change the sharing permissions for the entire thread, with the permission of all contributors of course, would be highly appreciated!)

As to why the question about Mechanical Turk generated so much useful information, there are three reasons I can think of.  The first is a simple affordance of the length of posts and comments.  Unlike twitter, detail can be provided when detail is required.  Whilst I have read the thoughts of writers praising the cognitive workout required to condense their tweets to be both eloquent and informative, it is limited medium that doesn’t lend itself to information-rich content or detailed evaluation.  Google+provides a clean, long-format forum in which ideas can be effectively transferred.

The second reason lies in the flexibility of the medium to provide relevant information to those who care.  Circles can be used to selectively share updates with certain groups.  This means that scientific updates can be restricted to my ‘Science’ circle, posts on running can be restricted to my ‘Runners’ circle,  and users may be feeling the effects of a more targeted dose of updates and information.  Comments aren’t driven by a desire to appear funny to a large number of people who probably share your boredom at the fact that, as it’s Sunday, Akira has once again completed a 6.3 mile run in a smidgen over 50 minutes – you’d probably only reach 5 people who would actually be rather preoccupied with trying to work out why Akira hasn’t managed to improve on his 6-mile time despite having done the same run every week for about 6 months.  Depending on your willingness to invest time in the categorisation of contacts, you can be taken as seriously as you want.

Finally, and maybe most importantly, Google+ is current rife with early-adopters. These are technologically ‘switched-on’ folk, who are willing to take a punt on a new medium, testing its capabilities and its uses as they go. To illustrate, Tom Hartley, Tal Yarkoni and Yana Weinstein all maintain current blogs/websites of their own and all contributors to the above thread are active twitter users (and well worth following).  Asking a question about how to conduct science using a nascent technology via a nascent communication technology stood every chance of being successful given the overlap in the Venn diagram of technology users.  Add to that the diminished risk of being called out as a ‘geek’, we’re all geeks here even before uber-geeks are further isolated within the ‘Geek’ circle, and we have the optimum conditions in which to find out about Amazon’s Mechanical Turk.

This isn’t to say that Google+ won’t be successful for non-technological academic discussion, or for technological discussion even after the the laggards arrive.  But I think that success depends on the parameters for its use in academia being established now.  If academics recognise that Google+ can be used to exchange work-related ideas early on in its life-cycle, then it has a much better chance of taking off and even being further developed with this use in mind. It already seems to me a far more attractive site for academics than academia.edu which has comprehensively failed to do anything other than act as a repository for electronic papers and CVs.

So, I’m quietly optimistic… until the next big thing comes along and I jump ship, desperately trying to keep up with all the other early-adopters.

[youtube http://www.youtube.com/watch?v=suJgV9HhJp8]