O'Really?

August 20, 2012

Digital Research 2012: September 10th-12th at St. Catherine’s College, Oxford, UK

Filed under: conferences,engineering,publishing,Science,technology,web of science — Duncan Hull @ 12:09 pm
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The Radcliffe Camera, Oxford by chensiyuan

The Radcliffe Camera, Oxford by chensiyuan via wikipedia

The UK’s premier Digital Research community event is being held in Oxford 10-12 September 2012. Come along to showcase and share the latest in digital research practice – and set the agenda for tomorrow at Digital Research 2012. The conference features an exciting 3-day programme with a great set of invited speakers together with showcases of the work and vision of the Digital Research community. Here are some highlights of the programme – please see the website digital-research.oerc.ox.ac.uk for the full programme and registration information.

New Science of New Data Symposium and Innovation Showcase  on Monday 10th: Keynotes from Noshir Contractor [1] (Northwestern University) on Web Science, Nigel Shadbolt (Government Information Adviser) on Open Data and a closing address by Kieron O’Hara (computer scientist) – with twitter analytics, geolocated social media and web observatories in between. Also the launch of the Software Sustainability Institute’s Fellows programme and community workshops.

Future of Digital Research on Tuesday 11th: Keynotes from Stevan Harnad on “Digital Research: How and Why the Research Councils UK Open Access Policy Needs to Be Revised” [2], Jim Hendler (Rensselaer Polytechnic Institute) on “Broad Data” (not just big!), and Lizbeth Goodman (University College Dublin) on “SMART spaces by and for SMART people”. Sessions are themed on Open Science with a talk by Peter Murray-Rust, Smart Spaces as a Utility and future glimpses from the community, all culminating in a Roundtable discussion on the Future of Digital Research.

e–Infrastructure Forum and Innovation Showcase on Wednesday 12th opens with a dual-track community innovation showcase, then launch the UK e-Infrastructure Academic Community Forum where Peter Coveney (UK e-Infrastructure Leadership Council and University College London) will present the “state of the nation” followed by a Provider’s Panel, Software, Training and User’s Panel – an important and timely opportunity for the community to review current progress and determine what’s needed in the future.

There’s a lot more happening throughout the event, including an exciting “DevChallenge” hackathon run by DevCSI, software surgery by the Software Sustainability Institute (SSI) and multiple community workshops – plus the Digital Research 2012 dinner in College and a reception in the spectacular Museum of Natural History in Oxford. Digital Research 2012 is very grateful to everyone who has come together to make this event possible, including e-Research South, Open Knowledge Foundation, Web Science, the Digital Social Research programme, our Digital Economy colleagues and the All Hands Foundation.

We look forward to seeing you at Digital Research 2012 in Oxford in September.

References

  1. Lazer, D., Pentland, A., Adamic, L., Aral, S., Barabasi, A.L., Brewer, D., Christakis, N., Contractor, N., Fowler, J., Gutmann, M. & (2009). Social Science: Computational Social Science, Science, 323 (5915) 723. DOI: 10.1126/science.1167742
  2. Stevan Harnad (2012). Open access: A green light for archiving, Nature, 487 (7407) 302. DOI: 10.1038/487302b

December 8, 2010

Science Careers: The Good, the Bad and the Starry

Filed under: education,web of science — Duncan Hull @ 6:03 pm
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Mauna Kea SunsetOf all the things you can do with a Science degree, being paid money to stargaze from the top of a volcano in Hawaiʻi has to be one of the more interesting.

Tom Kerr is one such lucky astronomer who has been managing operations at UKIRT (UK infrared telescope) – currently the world’s largest telescope dedicated solely to infrared astronomy [1]. So what is it like working more than 4000 metres* above sea level, near the summit of Mauna Kea on the big Island of Hawaiʻi? Can you imagine filling your days and nights  observing the glorious majesty of the night sky, amazing sunsets and sunrises interspersed with surfing sessions on the beach?

Tom’s blog A Pacific View documents what Hawaiian life can be like. A recent post things I’ll miss (and others I won’t) describes the good, bad and starry parts of astronomy in an exotic location. There is also an accompanying set of rather stunning pictures on Flickr. So if you’ve ever wondered what it’s like to be involved in stargazing for a living, Tom’s blog and photostream tells you more.

References

  1. Song, I., McCombie, J., Kerr, T., & Sarre, P. (2007). The 3.3-μm PAH emission band of the Red Rectangle Monthly Notices of the Royal Astronomical Society, 380 (3), 979-985 DOI: 10.1111/j.1365-2966.2007.12197.x and arXiv:0707.0541
  2. The interwebs is full of blogging astronomers …

[Creative Commons image of Mauna Kea Sunset by therefromhere, on Flickr]
*4000 metres is about 14,000 feet in real money…

May 28, 2010

The University of Twitter, UK: A Quick Survey

Filed under: web of science — Duncan Hull @ 7:23 am
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Twitter icon for a fluid app by Miha FilejMany people are still trying to work out exactly what twitter is good for [1] but with more than 100 million users worldwide making around 50 million tweets per day, the website is clearly popular with those who like to communicate via short “sound bites” of 140 characters or less.

Communication is an important part of what Universities are all about, so how many UK universities are on twitter? Knowing this could help us assess the use of the latest web technology in research where adoption has been rather limited so far, especially in Science  [2]. Rather than survey all the @UniversitiesUK, for a quick overview, let’s pick the twenty Russell Group Universities. According to their website, the Russell Group:

“represents the 20 leading UK universities which are committed to maintaining the very best research, an outstanding teaching and learning experience and unrivalled links with business and the public sector.”

So they are exactly the kind of places you would expect to be embracing and experimenting with new technology. The table below shows which of these institutions are on twitter:

@RussellGroup University @Twitter?
University of Birmingham @unibirmingham
University of Bristol @bristoluni
University of Cambridge @cambridge_uni
Cardiff University @cardiffuni
University of Edinburgh @uniofedinburgh
University of Glasgow @glasgowuni
Imperial College London @imperialcollege
King’s College London None as of May 2010*
University of Leeds @universityleeds
University of Liverpool @liverpoolfirst
London School of Economics None as of May 2010*
University of Manchester None as of May 2010*
Newcastle University None as of May 2010*
University of Nottingham @uniofnottingham
University of Oxford @uniofoxford
Queen’s University Belfast @queensubelfast
University of Sheffield @sheffielduni
University of Southampton @southamptonnews
University College London @uclnews
University of Warwick @warwickuni

There are plenty of important UK universities (@1994group, @UniAlliance, @million_plus etc) excluded from this quick-and-dirty survey but it gives us an idea of what is going on. As of May 2010, 16 out of 20 Russell Group Universities are on twitter – perhaps this is another reason to love Higher Education because it is full of twittering twits?

But the last words on the United Kingdom of Twitter should go to the @number10gov Prime Minister David Cameron who has enlightening views on twitter including this quote below:

“We complain about the sound bite culture [3] but if you think about it and go back in history sound bites have always been used. Do to others as you would be done by, that is a fantastic sound bite … If you can’t convey what you’re trying to convey in a few short sentences you’ve got a problem and you have a particular problem in the media age. You have to work at communicating something complicated in a simple way or you’re not going to take people with you.”

References

  1. Haewoon Kwak, Changhyun Lee, Hosung Park, & Sue Moon (2010). What is Twitter, a social network or a news media? WWW ’10: Proceedings of the 19th international conference on World Wide Web, New York, NY, USA, 591-600 DOI: 10.1145/1772690.1772751
  2. Amy Maxmen (2010). Science Networking Gets Serious Cell, 141 (3), 387-389 DOI: 10.1016/j.cell.2010.04.019
  3. David Slayden and Rita Kirk Whillock (1998). Soundbite Culture: The Death of Discourse in a Wired World. Sage Publications, Inc. ISBN:0761908722

* These Universities had no central account that I could find in May 2010 but some have departmental accounts like  @kingsbiomed, @kingsmedicine, @lsepublicevents, @lse_recruitment, @mcrmuseum and @manunicareers etc which are not counted here because they don’t represent the whole University in question. The University of Manchester has an account @UoMRSSFeed but it isn’t official and hasn’t been updated recently. Dear beloved Alma mater, sort it out!

[Creative commons licensed picture of Twitter icon for a fluid app via Miha Filej.]

May 21, 2010

myExperiment: The Videos

Filed under: informatics,Open Notebook Science,web of science — Duncan Hull @ 4:28 pm
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myExperiment is a research project that is exploring models, techniques and infrastructure for sharing digital items associated with  research , especially scientific workflows. The project is funded by the Joint Information Standards Committee (JISC) as part of a series of projects building Virtual Research Environments (VRE’s) and is run by Dave De Roure and Carole Goble at the Universities of Southampton and Manchester in the UK.

Last year, JISC made some professional videos describing the project. Needless to say, the videos were much more fun to make than the accompanying papers [1,2,3] and a probably more informative too. The best way of linking the research papers to the videos on youtube is to blog about them, so here they are. The first video (below) talks about the project generally:

The second video (below) discusses the data used in tackling African trypanosomiasis (sleeping sickness) in cattle.

The videos include interviews with Carole Goble, Dave De Roure, Paul Fisher, Andy Brass and yours truly.

References

  1. David De Roure, Carole Goble, & Robert Stevens (2007). Designing the myExperiment Virtual Research Environment for the Social Sharing of Workflows IEEE International Conference on e-Science and Grid Computing, 603-610 DOI: 10.1109/E-SCIENCE.2007.29
  2. David De Roure, Carole Goble, Jiten Bhagat, Don Cruickshank, Antoon Goderis, Danius Michaelides, & David Newman (2008). myExperiment: Defining the Social Virtual Research Environment IEEE Fourth International Conference on eScience, 2008. eScience ’08., 182-189 DOI: 10.1109/eScience.2008.86
  3. Goble, C., Bhagat, J., Aleksejevs, S., Cruickshank, D., Michaelides, D., Newman, D., Borkum, M., Bechhofer, S., Roos, M., Li, P., & De Roure, D. (2010). myExperiment: a repository and social network for the sharing of bioinformatics workflows Nucleic Acids Research DOI: 10.1093/nar/gkq429

April 8, 2010

Embracing Open Science

Filed under: Open Notebook Science,web of science — Duncan Hull @ 10:37 pm
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Open Push (Oklahoma, Manchester)There’s an interesting article [1] by Chelsea Wald in Science magazine published today, about Open Science including Open Source Code, Open Notebook Science, Open Data and Open Access Publishing.

It interviews some of the advocates and sceptics of a more open approach to doing Science, including:

It’s well worth a read, despite being a bit US-centric, and looks like it’s freely available via Open Access Publishing [2] too.

[Update: There is some follow-up commentary on the original article here and here]

References

  1. Chelsea Wald (2010). Scientists Embrace Openness Science (2010-04-09) DOI: 10.1126/science.caredit.a1000036
  2. Declan Butler (2010). US seeks to make science free for all Nature, 464 (7290), 822-823 DOI: 10.1038/464822a

September 10, 2009

Why don’t scientists share data?

Filed under: communication,publishing,Science,web of science — Duncan Hull @ 2:28 pm
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Sharing Ice Cream by ClappstarAs Vince Smith once put it [1] data are the fuel of Science:

“The fabric of science is changing, driven by a revolution in digital technologies that facilitate the acquisition and communication of massive amounts of data. This is changing the nature of collaboration and expanding opportunities to participate in science. If digital technologies are the engine of this revolution, digital data are its fuel. But for many scientific disciplines, this fuel is in short supply.”

Despite the importance of data, some scientists are often really bad at sharing it properly. So why don’t scientists share data?

Nature has a special issue dedicated to this topic published today at nature.com/news/specials/datasharing [2,3,4,5] which isn’t behind a pay wall (at the moment). It describes some of the technical and cultural barriers to data sharing. You should go and read it yourself if you’re interested, but here is a very brief and incomplete summary, with some extra points thrown in for good measure:

  • Some funding bodies do not adequately support the research projects they sponsor in sharing data properly, both before and after publication.
  • Many scientists lack awareness, incentives and knowledge of data sharing which can be compounded by a fear of being “scooped”.
  • Public databases, often a more natural home for data than traditional publications, are frequently undervalued by a publish or perish culture [6].
  • Traditional scientific publishing is frequently (and ironically) a really inadequate method for sharing data. Important data and metadata routinely gets damaged or destroyed in the process of publishing [7].
  • The technical infrastructure for long term data sharing either does not exist or is not understood by those who should be providing and using it. This can lead to empty archive syndrome.

These are some of the reasons that scientists don’t share data. Which raises the question, how do we get out of this mess? The special issue offers some solutions [3,4] to these cultural and technical problems, including the use of Creative Commons licenses. It’s good to see these important issues given a higher profile but we will probably be striving for better data sharing for many years to come.

References

  1. Vince Smith (2009). Data publication: towards a database of everything BMC Research Notes, 2 (1) DOI: 10.1186/1756-0500-2-113
  2. Anonymous (2009). Data’s shameful neglect: Research cannot flourish if data are not preserved and made accessible. Nature, 461 (7261), 145-145 DOI: 10.1038/461145a
  3. Schofield, P., Bubela, T., Weaver, T., Portilla, L., Brown, S., Hancock, J., Einhorn, D., Tocchini-Valentini, G., Hrabe de Angelis, M., & Rosenthal, N. (2009). Post-publication sharing of data and tools Nature, 461 (7261), 171-173 DOI: 10.1038/461171a
  4. Toronto International Data Release Workshop Authors (2009). Prepublication data sharing Nature, 461 (7261), 168-170 DOI: 10.1038/461168a
  5. Bryn Nelson (2009). Data sharing: Empty archives Nature, 461 (7261), 160-163 DOI: 10.1038/461160a
  6. Michael Seringhaus, & Mark Gerstein (2007). Publishing perishing? Towards tomorrow’s information architecture BMC Bioinformatics, 8 (1) DOI: 10.1186/1471-2105-8-17
  7. Duncan Hull, Steve Pettifer, & Douglas Kell (2008). Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web PLoS Computational Biology, 4 (10) DOI: 10.1371/journal.pcbi.1000204

[CC-licensed picture of Sharing by ryancr, more commentary on this post over at friendfeed.]

November 27, 2008

Blogging Professors: Douglas Kell at the BBSRC

Filed under: web of science — Duncan Hull @ 12:53 pm
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Biotechnology and Biological Sciences Research CouncilTo add to the growing list of big boffins with blogs, Professor Douglas Kell has launched his BBSRC hosted blog. So has blogging finally gone from an innovative underground movement to grown-up mainstream everyday technology, as recently suggested in The Economist? How many more senior scientists might we see blogging in the future? Take a look at blogs.bbsrc.ac.uk to find out..

I asked Doug if he would consider blogging, for the Science blogging challenge posed by Nature Publishing Group, so thanks Doug for being open minded and willing to experiment, you’ve also been entered for the Open Laboratory 2008 competition too. It will be interesting to see what the result of this project will be…

References

  1. Zoe Corbyn (2008). New BBSRC chief executive enters blogosphere, Times Higher Education, 11th December 2008.

November 24, 2008

Embracing Registries of Web Services

Filed under: informatics,web of science — Duncan Hull @ 2:00 pm
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Embracing by tanakwhoIf you travel back in time, to around 2002, it isn’t difficult to find people claiming that Web services were going to be the new silver bullet technology to create world peace, eradicate global poverty and finally make some sense of all the data produced by the human genome project. Over hyped? Just a bit. One of the many reasons none of these things happened, is it turned out to be much harder than anticipated to build centralised registries, where people could go to find Web services to perform a given task. Can service registries ever be built? Critics like Tim Bray at Sun Microsystems for example, have suggested that (quote) “registries are a fantasy”, but some already exist and there are more in the pipeline. This article briefly introduces some of them: Seekda, BioMOBY, the Embrace service registry and the Biocatalogue project. (more…)

October 31, 2008

Defrosting the Digital Library

Filed under: web of science — Duncan Hull @ 7:21 am
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Bibliographic Tools for the Next Generation Web

Sunset Ice Sculptures by Mark K.We started writing this paper [1] over a year ago, so it’s great to see it finally published today. Here is the abstract:

“Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as “thought in cold storage,” and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.”

Biotechnology and Biological Sciences Research CouncilThanks to Kevin Emamy, Richard Cameron, Martin Flack, and Ian Mulvany for answering questions on the CiteULike and Connotea mailing lists; and Greg Tyrelle for ongoing discussion about metadata and the semantic Web nodalpoint.org. Also thanks to Timo Hannay and Tim O’Reilly for an invitation to scifoo, where some of the issues described in this publication were discussed. Last but not least, thanks to Douglas Kell and Steve Pettifer for helping me write it and the BBSRC for funding it (grant code BB/E004431/1 REFINE project). We hope it is a useful review, and that you enjoy reading it as much as we enjoyed writing it.

References

  1. Duncan Hull, Steve Pettifer and Douglas B. Kell (2008). Defrosting the digital library: Bibliographic tools for the next generation web. PLoS Computational Biology, 4(10):e1000204+. DOI:10.1371/journal.pcbi.1000204, pmid:18974831, pmcid:2568856, citeulike:3467077
  2. Also mentioned (in no particular order) by NCESS, Wowter, Twine, Stephen Abram, Rod Page, Digital Koans, Twitter, Bora Zivkovic, Digg, reddit, Library Intelligencer, OpenHelix, Delicious, friendfeed, Dr. Shock, GribbleLab, Nature Blogs, Ben Good, Rafael Sidi, Scholarship 2.0, Subio, up2date, SecondBrain, Hubmed, BusinessExchange, CiteGeist, Connotea and Google

[Sunrise Ice Sculptures picture from Mark K.]

October 14, 2008

Open Access Day: Why It Matters

Filed under: web of science — Duncan Hull @ 12:16 am
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Open Access Day 14th October 2008Today, Tuesday the 14th of October 2008, is Open Access Day. Like many others, this blog post is joining in by describing why Open Access matters – from a personal point of view. According to the wikipedia article Open Access (OA) is “free, immediate, permanent, full-text, online access, for any user, web-wide, to digital scientific and scholarly material, primarily research articles published in peer-reviewed journals. OA means that any individual user, anywhere, who has access to the Internet, may link, read, download, store, print-off, use, and data-mine the digital content of that article. An OA article usually has limited copyright and licensing restrictions.” What does all this mean and why does it matter? Well, in four question-and-answer points, here goes… (more…)

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