June 2013 - Weeding the Gems

Two GARNet Events

by Charis Cook

Categories: bioinformatics, Friday Film, GARNet, Workshops

Tags: bioinformatics, GARNet workshop, iPlant, next generation sequencing

Comments: 1 Comment

Published on: June 21, 2013

Image by Centimedia.org for GARNet

We have some GARNet news to share!

First of all, we are pleased to finally open registration for the hands-on iPlant training workshop ‘Data Mining with iPlant‘. Unfortunately we’ve had to change the planned location, and it will now be at the University of Warwick. The date is still 17-20 September 2013.

For those who don’t know, iPlant is an incredible free resource which allows its users to access high performance computing power, large scale data storage, and analytical software needed for a variety of data- or compute- intensive research applications.

You can either come for just one day for a free hands-on introduction to iPlant, or stay for four days and get in depth training on how to analyse real data in iPlant. For more information go to: http://www.garnetcommunity.org.uk/news/13-06-19/data-mining-iplant-17-20-september-2013

Our second announcement is more of a save-the-date than an invitation. The GARNet general conference will return next year, possibly for one time only. GARNet 2014: The Past, Present and Future of the Genetic Model Revolution will be held at the University of Bristol on 9-10 September 2014. It will be a celebration of exciting new plant science, and a look at the evolving nature of model systems as well as the brilliant achievements made with them in the past.

The Journal of Experimental Botany kindly recorded and uploaded talks from the last GARNet conference in 2011. Here is Katherine Denby of the University of Warwick talking about the PRESTA project, which since this talk has produced two Plant Cell papers (1,2). You can see the rest of the talks from GARNet 2011 on the JXB website.

Open access: How much is enough?

by Charis Cook

Categories: Open Access

Tags: BBSRC, Open Access

Comments: No Comments

Published on: June 4, 2013

Nearly everyone is behind Open Access as an idea, but when RCUK demanded that all papers published from RCUK-funded groups be published open access it became clear that widespread, truly open access publication is still an idea and not a deliverable. The problem is that while scientists see the moral case for open access, and it is to their advantage to have as wide an audience as possible for their research, open access publishing can be extremely expensive, especially when academic careers are so invested in publications in high-impact, traditionally high-profile journals.

Open Access publishing can be cheap – national journals can even be free, though according Eigenfactor, there are no UK-based free plant science journals. PloS and BMC are charging around £1200 per article. When I looked up the OA fee on the BMC website, a friendly message popped up saying that the University of Warwick would pay half the publication fee if I submitted an article to them; other institutions will have similar schemes to help with payment of publication costs. Plant Physiology charge £750 for OA publication, though this is on top of often much larger pre-existing fees for colour publication and other costs. These figures seem reasonably affordable with the planned block grants to provide funding for article processing charges.

Article processing charges (APC) funding will come into force in academic year 2013/14, and during this time research institutions are expected to make sure 45% of papers are published OA. In mid 2014 the funding mechanism will be reviewed. Over the next few years, it is expected that the proportion of OA articles will go up – the target for 2014/15 is 53% at the time of writing.

However, I have heard from several people that some journals are charging a very high fee for OA publishing – in excess of £10 000. The APC fund will not be able to cover fees as large as that. So it is good news then that in April of this year, RCUK revised the original announcement that OA publication means ‘gold’ – ‘green’ OA is acceptable. This means that you can publish your work in many journals without paying the OA fee, and self-publish the paper in a format and forum agreed to by the publisher. In most cases this means you can put a non-formatted version of the accepted article on your website and in your institutional repository.

While researching this post on Open Access (OA), I found these webpages which will be of use to anyone who is confused about the RCUK OA policy:

Sherpa is an online tool from RCUK that explains users’ options for complying with their policy in the majority of journals. For example, if you search for ‘New Phytologist’ it explains that you can pay $3000 for the gold open access option, OR archive your article in an open access repository.
A commentary from The Times about April’s revision to RCUK’s OA policy.
RCUK’s Policy on Open Access FAQs (PDF) – you might not get as must detail as you want about the future of the OA policy, but this is the first place you should check if you have questions.
Stephen Curry regularly blogs about open access, and is one of the reasons RCUK had to clarify their stance on the importance of impact factors as a result of their OA policy – well worth a read.

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