Quantum Earth and Paperscape: mapping arXiv

Copyright Roberto Salazar & Sebastian Pizarro

Above is a visualisation of Quantum Earth, a continent consisting of research articles in the field of quantum mechanics. The idea was originally conceived by Roberto Salazar after completing his PhD on quantum information at the University of Concepción in Chile. Roberto teamed up with Sebastian Pizarro a digital designer to bring his idea of a quantum mechanics continent to life. The result was a map reminiscent of Tolkein replete with geographic landmarks such as Teleportation Lake and Quantum Engineering Volcano.


We contacted Roberto for his thoughts on open access:

"I think open access publishing is the way that things should be done in science. That being said, I feel that this will happen only if we improve open access tools for finding the right paper for your research. In this sense I believe that Paperscape is a breakthrough in the field and hope that it will be the first of many more. I use it in my daily research and has been of great help in finding the right paper and saving time (I just love it).

Our little contribution with the "Quantum Earth" map, is to give a graphic idea of how to use Paperscape when you already have an insight in the field. Also the purpose is to give positive publicity to this great idea."

Copyright Damien George and Rob Knegjens. Downloaded here

Paperscape is a project developed by Damien George and Rob Knegjens, two post doctoral researchers who wanted to create a tool to visualise the huge volume of papers in the pre-print repository arXiv. Visually, Paperscape resembles a galaxy made up of over a million stars. Each of the 'stars' represent actual research articles in the arXiv repository. The positions of the articles are determined by references to other articles, and in effect the references act as a gravitational force in the Paperscape galaxy, pulling closely related articles together to form clusters. The way the tool structures the articles makes finding new and highly cited articles much easier as well. This is because highly cited articles appear larger and new articles appear brighter.

Posters of the Paperscape galaxy are freely available to download here in various sizes.
The full size Quantum Earth map can be viewed and downloaded here.

Repositories: extending the reach of research

Repositories such as our own Research@StAndrews:FullText are a great way to increase the visibility of research. It is also a way to extend the reach of research to those unable to afford the pricey subscriptions demanded by many publishers.

A great example of the benefits of depositing manuscripts in Research@StAndrews:FullText is Forgiving you is hard, but forgetting seems easy: can forgiveness facilitate forgetting? by Saima Noreen,  Raynett Bierman, and Malcolm David MacLeod.

The paper can be found in Research@StAndrews:FullText here http://hdl.handle.net/10023/4779.

Many people won't go directly to our repository to find content, but will instead rely on Google. The Google search results clearly show the favourable rankings of Research@StAndrews:FullText; of the 30,000 results the repository is ranked 2nd. So, someone looking to read the article might be inclined to click on the first link and go to publisher source first. However, upon clicking that link, unless they have a subscription they will be met with a pay-wall. This pay-wall is particularly expensive at $35 for a mere 24 hours!

So, repositories like Research@StAndrews:FullText provide the second option: an accepted manuscript with all the same information as the published version, but free of charge (and with no time constraints!)

The Repository: helping to feed the impact of research

Over the years, the OARPS team has spent a great deal of time acquiring academic manuscripts and releasing them to the world through the repository.

Much of our current work involves assisting academics with complying with funder open access mandates. For instance, the RCUK mandate states that RCUK funded research papers should be made Open Access either by choosing "Gold" and paying an APC charge, or by choosing "Green" and uploading the accepted manuscript of the final article to Pure (and then the library can transfer the paper to the repository).

Presently, the team focus has incorporated the new HEFCE open access policy for the next REF as well. The HEFCE open access policy states that in order to be eligible, the accepted manuscripts of articles and conference proceedings (with an ISSN) must be deposited in a repository. The HEFCE open access policy does not come into effect until 2016, but we are tying to push the message now so that we are 100% compliant by that point.

With both these cases the result is more content in the repository. But with deposit being imposed from on high the other benefits of depositing can sometimes play second fiddle. In light if this, we have chosen to show some of the usage metrics from a recent article in the repository. We hope this demonstrates that archiving in the repository can greatly benefit the Impact of research.

A great example is The meanings of chimpanzee gestures which received a lot of media attention when it was published. The authors deposited the accepted manuscript for the article into Pure, which then allowed the OARPS team to get the manuscript into the repository.

Here are some of the repository usage stats for the article:

With statistics like this you have to read between the lines a little bit, but one thing they definitely show is that the article received a lot of attention in July (this was when the article was being covered in the media). Crucially, the stats also tell us that the vast majority of those visiting the page ended up downloading the document. This reliably indicates that the majority of people visiting the page did not have access to the publisher version.

So, with the manuscript in the repository a wider range of people, who do not have a subscription to the journal, can read the full article. This means it can be distributed more widely through society, thus widening the reach of the paper and helping to feed the impact of the research.

Open access home for St Andrews housing report

The Centre for Housing Research at the University of St Andrews released a new report just before the end of 2013. 'Growing economies and building homes: Reconciling growth and housing wellbeing in St Andrews' examines the impacts of University led growth on the rental housing market in North East Fife. A University press release noted:

The study has found while the success and growth of the 600-year-old University has brought prosperity and employment to Fife, existing pressures on local housing have been increased by an influx of students and staff.

This has added to the disadvantage experienced by some in the local community, most importantly, people on low incomes who have had to look further and further from St Andrews in the search for affordable accommodation.

The CHR report raises important issues and was read with great interest by staff in the Library. In order to ensure high visibility and a permanent home, the report is now available from our institutional repository. We hope that this will encourage further interest in the local community, and we will be able to track usage through our embedded statistics feature.


Maclennan, D, O'Sullivan, T, Maynard, K, Sila-Nowicka, K & Walden, Y. 2013. Growing economies and building homes: Reconciling growth and housing wellbeing in St Andrews. University of St Andrews. http://hdl.handle.net/10023/4316

Impact of open access on teaching

During this year's Open Access Week, BioMed Central highlighted a number of open access articles that address questions of impact on society. Having just caught up with the collected tweets, we are delighted to see an article in BMC Bioinformatics by St Andrews authors Daniel Barker et al. mentioned as a way that open access can benefit the public:

.@univofstandrews lecturers use @raspberrypi & #OpenAccess materials to teach bioinformatics http://t.co/PZLjSxUdKw #OAWeek #imFact
— BioMed Central (@BioMedCentral) October 23, 2013

The article is about teaching bioinformatics to biologists at the University of St Andrews with a low-cost computing environment, and an embedded open access course:

By including an explicit Open Access licence, and removing or replacing material incompatible with this from 4273π Bioinformatics for Biologists, we have been able to share it with anyone interested, the world over, in such a way that they can – with minimal care – re-use and adapt it without accusation of plagiarism or copyright violation.

The article is of course open access itself, paid for by the University's membership of BioMed Central

The full list of stories are available from the BioMed Central blog

Celebrating Open Access @ St Andrews

We are always delighted at the wealth of content we discover through our open access services, and the insight we get on the amazing research going on in our academic community. To celebrate this, we have created a range of bookmarks with images illustrating some items in our repository. The first three in the series are shown below, and we will be adding more soon.

 Image from Byrne, RW, Bates, L & Moss, CJ 2009, 'Elephant cognition in primate perspective' Comparative Cognition & Behavior Reviews, vol 4, pp. 65-79. http://hdl.handle.net/10023/1612 

Image from Jaeger, A, Selmeczy, D, O'Connor, AR, Diaz, M & Dobbins, I 2012, 'Prefrontal cortex contributions to controlled memory judgment: fMRI evidence from adolescents and young adults' Neuropsychologia, vol 50, no. 14, pp. 3745-3756. http://hdl.handle.net/10023/3243

Image by Tiago Marques, fieldwork for: Aars, J, Marques, TALO, Andersen, M, Belikov, S, Boltunov, A, Buckland, ST & Wiig, O 2009, 'Estimating the Barents Sea polar bear subpopulation size' Marine Mammal Science, vol 25, no. 1, pp. 35-52. http://hdl.handle.net/10023/1879

 

3000 items and the open access cake

In what is becoming a regular summer event, this week we celebrated another landmark for our open access repository with the 3000th item made available in Research@StAndrews:FullText

Akira O’Connor deposited a version of his paper in our Research Information System, Pure, in order to make it open access. The publisher of the Journal of Cognitive Neuroscience, MIT Press, allows authors to archive the final version of their article after a short embargo.

“In the JoCN paper, we report an experiment in which we scanned people's brains as they were completing a memory task. Using these fMRI scans, we were able to show that the left ventrolateral prefrontal cortex (a region of the brain's surface near your left temple) is actually involved in processing the meaning of words, rather than directly involved in memory retrieval as was previously thought.”

Dr O’Connor already has a number of open access papers in Research@StAndrews:FullText: in most cases these are his accepted manuscripts, the version most commonly allowed by publishers. His latest paper is currently submitted to an open access journal, Frontiers in Psychology. When told about our latest landmark, he contacted us to say:

“That the library has put so much effort into making our work accessible to all is something I'm very proud of. The OA fund and Research@StAndrews:FullText provide a range of options for St Andrews researchers to publish their work in the most suitable journal whilst also acknowledging that the way scholarly output is disseminated is changing. It's a comprehensive approach to open access and I look forward to seeing it go from strength to strength.”

UPDATE: More on open access from Akira O'Connor's blog

The ‘3000’ spot was narrowly missed by an open access article in PLoS ONE, which has been added to our repository under a Creative Commons Licence. The lead author of this paper, PhD student Joana Carvalho, is supervised by co-author Dr Tiago Marques, who also has a number of research outputs in the repository and has previously featured in our blog. This new article describes a study of the population status of the western chimpanzee, Pan troglodytes verus, which has been classified as an Endangered species.

Other recent open access items contributed to the repository include Phd theses:
How terrorism ends : understanding the outcomes of violent political contestation by Sarah V Marsden
The victims of a sorted life : ageing and caregiving in an American retirement community by Philip Y Kao
and journal articles:
Policy change and learning in the RBC model by Kaushik Mitra, George W Evans and Seppo Honkapohja
4273π : bioinformatics education on low cost ARM hardware by Daniel Barker et al.

We will be organising a ‘champagne moment’ soon with our winning author by way of celebration. In the meantime Library staff took a few minutes out to share some open access cake. Not only has our content grown since 2010 - so has our cake!

Open access cake 2010

Open access cake 2013

University Librarian John MacColl

BBC request St Andrews thesis

Every student to pass through St Andrews leaves a legacy in one form or another, and for our postgraduates this often takes the shape of a thesis. The university requires students to submit a copy of their thesis to the library in order to graduate, but who is it that might end up reading your precious creation, years or even decades after you have gone?

Well, you’ll be pleased to know they’re not just propping up the desks here in the underbelly of the library where the repository work takes place, and unfortunately they make for rather unwieldy coasters. In reality, whether in digital or print form they are a tangible monument to our university’s research excellence, and recently an urgent call came through from the BBC. It’s not unusual for us to receive requests for viewings from scholars around the country, primarily through the British Library’s EThOS service, but last month the team behind ‘Coast’ requested a copy of F. M. Fraser’s 1977 PhD thesis: ‘The Lewisian and Torridonian geology of Iona’ – on the double!

With a tight filming schedule on Iona to be met, there was no time to send it off to London for digitisation as would usually happen, and so it was rushed off to Special Collections to be scanned in-house. One week later we presented the BBC with four hundred pages of geographical goodness, saving the day by assuring there would be sufficient educational content to match the moody shots of Neil Oliver’s locks flapping about in the wind. Whoever said that library work isn’t glamorous?

Season 9 of ‘Coast’ will be hitting our screens in 2014, but for the keener amongst you, here is a link to Dr Fraser’s thesis in Research@StAndrews:FullText:
http://hdl.handle.net/10023/3812

Heather Curtis (Guest blogger & intern)

Landmark 1000 items in repository

We have now reached a landmark total of 1000 items in Research@StAndrews: Full text, the University's digital research repository. 

 

We will be featuring a number of theses and research publications that have contributed to this milestone over the next few weeks. Congratulations to all our authors whose work is now reaching a wider audience!

Most viewed items in Research@StAndrews:FullText

The article by Len Thomas Retrospective power analysis remains the most highly accessed article in Research@StAndrews:FullText, with 170 views in May 2011.

Also frequently viewed, our first thesis by portfolio to be deposited has proved of interest with 74 views:

The inferior vena caval compression theory of hypotension in obstetric spinal anaesthesia: studies in normal and preeclamptic pregnancy, a literature review and revision of fundamental concepts

The rest of the top 10 most viewed items are shown below.
The soft-focus lens and Anglo-American pictorialism
Saint Peter and Paul Church (Sinan Pasha Mosque), Famagusta: a forgotten Gothic moment in Northern Cyprus
Understanding barriers to small business growth from the perspective of owner-managers in Russia
Global distributive justice
The consequences of Israel's counter terrorism policy
What is social learning?
Applications of microfluidic chips in optical manipulation & photoporation
Karl Barth's academic lectures on Ephesians (Göttingen, 1921-1922)

Public visibility for St Andrews research activity

A new portal showcasing the excellent research at University of St Andrews, Research@StAndrews, is now publicly available from the University's Research pages.




The Research@StAndrews portal features activities, researcher profiles, links to Schools and research publications.