O'Really?

April 1, 2014

The Serene Scientists Serenity Prayer via Jon Butterworth

banksy church

The Church of Banksy

Whatever your religous preferences, the Serenity Prayer by Reinhold Niebuhr captures a certain wisdom about life in general. So it is good to see that physicist Jon Butterworth at UCL has adapted it [1] for scientists:

“Give me grace to accept with serenity the things that cannot be understood,

Data to investigate the things which can be understood,

And the Wisdom to know the difference.”

Amen!

References

  1. Jon Butterworth (2014) Giles Fraser says scientists are replacing theologians. Some thoughts on that The Gruaniad, 2014-03-31

January 18, 2013

How to export, delete and move your Mendeley account and library #mendelete

Deleteme

Delete. Creative Commons licensed picture by Vitor Sá – Virgu via Flickr.com

News that Reed Elsevier is in talks to buy Mendeley.com will have many scientists reaching for their “delete account” button. Mendeley has built an impressive user-base of scientists and other academics since they started, but the possibility of an Elsevier takeover has worried some of its users. Elsevier has a strained relationship with some groups in the scientific community [1,2], so it will be interesting to see how this plays out.

If you’ve built a personal library of scientific papers in Mendeley, you won’t just want to delete all the data, you’ll need to export your library first, delete your account and then import it into a different tool.

Disclaimer: I’m not advocating that you delete your mendeley account (aka #mendelete), just that if you do decide to, here’s how to do it, and some alternatives to consider. Update April 2013, it wasn’t just a rumour.

Exporting your Mendeley library

Open up Mendeley Desktop, on the File menu select Export. You have a choice of three export formats:

  1. BibTeX (*.bib)
  2. RIS – Research Information Systems (*.ris)
  3. EndNote XML (*.xml)

It is probably best to create a backup in all three formats just in case as this will give you more options for importing into whatever you replace Mendeley with. Another possibility is to use the Mendeley API to export your data which will give you more control over how and what you export, or trawl through the Mendeley forums for alternatives. [update: see also comments below from William Gunn on exporting via your local SQLite cache]

Deleting your Mendeley account #mendelete

Login to Mendeley.com, click on the My Account button (top right), Select Account details from the drop down menu and scroll down to the bottom of the page and click on the link delete your account. You’ll be see a message We’re sorry you want to go, but if you must… which you can either cancel or select Delete my account and all my data. [update] To completely delete your account you’ll need to send an email to privacy at mendeley dot com. (Thanks P.Chris for pointing this out in the comments below)

Alternatives to Mendeley

Once you have exported your data, you’ll need an alternative to import your data into. Fortunately, there are quite a few to choose from [3], some of which are shown in the list below. This is not a comprehensive list, so please add suggestions below in the comments if I missed any obvious ones. Wikipedia has an extensive article which compares all the different reference management software which is quite handy (if slightly bewildering). Otherwise you might consider trying the following software:

One last alternative, if you are fed up with trying to manage all those clunky pdf files, you could just switch to Google Scholar which is getting better all the time. If you decide that Mendeley isn’t your cup of tea, now might be a good time to investigate some alternatives, there are plenty of good candidates to choose from. But beware, you may run from the arms of one large publisher (Elsevier) into the arms of another (Springer or Macmillan which own Papers and ReadCube respectively).

References

  1. Whitfield, J. (2012). Elsevier boycott gathers pace Nature DOI: 10.1038/nature.2012.10010
  2. Van Noorden, R. (2013). Mathematicians aim to take publishers out of publishing Nature DOI: 10.1038/nature.2013.12243
  3. Hull, D., Pettifer, S., & Kell, D. (2008). Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web PLoS Computational Biology, 4 (10) DOI: 10.1371/journal.pcbi.1000204
  4. Attwood, T., Kell, D., McDermott, P., Marsh, J., Pettifer, S., & Thorne, D. (2010). Utopia documents: linking scholarly literature with research data Bioinformatics, 26 (18) DOI: 10.1093/bioinformatics/btq383

August 20, 2012

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

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

August 3, 2012

May 11, 2012

Journal Fire: Bonfire of the Vanity Journals?

Fire by John Curley on Flickr

Fire by John Curley, available via Creative Commons license.

When I first heard about Journal Fire, I thought, Great! someone is going to take all the closed-access scientific journals and make a big bonfire of them! At the top of this bonfire would be the burning effigy of a wicker man, representing the very worst of the vanity journals [1,2].

Unfortunately Journal Fire aren’t burning anything just yet, but what they are doing is something just as interesting. Their web based application allows you to manage and share your journal club online. I thought I’d give it a whirl because a friend of mine asked me what I thought about a paper on ontologies in biodiversity [3]. Rather than post a brief review here, I’ve posted it over at Journal Fire. Here’s some initial thoughts on a quick test drive of their application:

Pros

On the up side Journal Fire:

  • Is a neutral-ish third party space where anyone can discuss scientific papers.
  • Understands common identifiers (DOI and PMID) to tackle the identity crisis.
  • Allows you to post simple anchor links in reviews, but not much else, see below.
  • Does not require you to use cumbersome syntax used in ResearchBlogging [4], ScienceSeeker and elsewhere
  • Is integrated with citeulike, for those that use it
  • It can potentially provide many different reviews of a given paper in one place
  • Is web-based, so you don’t have to download and install any software, unlike alternative desktop systems Mendeley and Utopia docs

Cons

On the down side Journal Fire:

  • Is yet another piece social software for scientists. Do we really need more, when we’ve had far too many already?
  • Requires you to sign up for an account without  re-using your existing digital identity with Google, Facebook, Twitter etc.
  • Does not seem to have many people on it (yet) despite the fact it has been going since at least since 2007.
  • Looks a bit stale, the last blog post was published in 2010. Although the software still works fine, it is not clear if it is being actively maintained and developed.
  • Does not allow much formatting in reviews besides simple links, something like markdown would be good.
  • Does not understand or import arXiv identifiers, at the moment.
  • As far as I can see, Journal Fire is a small startup based in Pasadena, California. Like all startups, they might go bust. If this happens, they’ll take your journal club, and all its reviews down with them.

I think the pros mostly outweigh the cons, so if you like the idea of a third-party hosting your journal club, Journal Fire is worth a trial run.

References

  1. Juan Carlos Lopez (2009) We want your paper! The similarity between high-end restaurants and scientific journals Spoonful of Medicine, a blog from Nature Medicine
  2. NOTE: Vanity journals should not to be confused with the The Vanity Press.
  3. Andrew R. Deans, Matthew J. Yoder & James P. Balhoff (2012). Time to change how we describe biodiversity, Trends in Ecology & Evolution, 27 (2) 84. DOI: 10.1016/j.tree.2011.11.007
  4. Shema, H., Bar-Ilan, J., & Thelwall, M. (2012). Research Blogs and the Discussion of Scholarly Information PLoS ONE, 7 (5) DOI: 10.1371/journal.pone.0035869

April 2, 2012

Open Data Manchester: Twenty Four Hour Data People

Sean Ryder at the Hacienda by Tangerine Dream on flickr

Sean Ryder, the original twenty-four hour Manchester party person of the Happy Mondays, spins the discs at the Wickerman festival in 2008. Creative commons licensed image via Tangerine Dream on flickr.com

According to Francis Maude, Open Data is the raw material for “next industrial revolution”. Now you should obviously take everything politicians say with a large pinch of salt (especially Maude) but despite the political hyperbole, when it comes to data he is onto something.

According to wikipedia, which is considerably more reliable than politicians, Open Data is:

“the idea that certain data should be freely available to everyone to use and republish as they wish, without restrictions from copyright, patents or other mechanisms of control.”

Open Data is slowly having an impact in the world of science [1] and also in wider society. Initiatives like data.gov in the U.S. and data.gov.uk in England, also known as e-government or government 2.0, have put huge amounts of data in the public domain and there is plenty more data in the pipeline. All of this data makes novel applications possible, like cycling injury maps showing accident black spots, and many others just like it.

To discuss the current status of Open Data in Greater Manchester there were two events last week:

  1. The Open Data Manchester meetup “24 hour data people” [2] at the the Manchester Digital Laboratory (“madlab”), which recently made BBC headlines with the DIY bio project
  2. The Discover Open Data event at the Cornerhouse cinema
Here is a brief and incomplete summary of what went on at these events:

(more…)

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