Tuesday, July 31, 2012

Recent Literature on Lichens - A New Approach

Recently, I took over as the lead author of the Recent Literature on Lichens (RLL) publication series in The Bryologist.  I want to thank Bob Egan for all of his work over the past many years putting together these lists!  I also thank Sarah Hodkinson, my wife and Master of Library Science, for taking over in the interim while I was finishing up my dissertation work and for staying on as a co-author.  Although RLL may seem pretty much the same on the surface, there have been many changes over the past year going on behind the scenes.  It's finally reached the point where there is a stable set of protocols, thanks to a lot of help from Einar Timdal, who has been working to reconfigure the long-standing RLL database so that it can be updated instantaneously, with citations of recent literature appearing online even before the literature lists are submitted for publication.

The main motivations for changing the RLL protocols were (1) to make it possible to add citations to the list from any computer connected to the internet, (2) to open up the possibility of having multiple authors, and (3) to ensure that citations could become available immediately to the community.  Previously, RLL lists were assembled using the proprietary software EndNote, which is an excellent tool for citation management.  However, this meant that the library of citations typically had to be kept as a single document on a single computer that had the software installed.  Also, the citations needed to be exported in batches and uploaded to the public RLL database every so often.  The procedure now involves adding citations to the online database immediately, either through manual web-form entry or RIS-formatted citation imports.  This means that if one searches the database at http://nhm2.uio.no/botanisk/lav/RLL/RLL.HTM and keeps the "Work file" box checked, it will be possible to see the most recent literature citations that have just been entered into the database.  When it is time to send in the publication, I can export the citations in a format appropriate for The Bryologist, and paste them into the newest manuscript.

Although the workflow seems relatively simple and straightforward, a great deal of 'curation' is still necessary.  However, the procedure meets the goals of portability, flexibility, and accessibility... and it has worked extremely well for the first few lists!

- Brendan

Saturday, July 21, 2012

Summer Conferences

It has been a busy month so far! I have attended two conferences this month, giving a talk and presenting a poster at each. The first was the annual Botany conference ("Botany 2012: The Next Generation") in Columbus, Ohio. There were some great talks and a lot of buzz about "next-gen" sequencing technologies (in keeping with the conference's subtitle).  I gave a talk about using next-gen sequencing for elucidating the phylogeny and resolving the taxonomy of sterile crustose lichens. I also discussed the utility of our data sets for examining fungal communities associated with lichens. The poster that I presented put my work in the broader context of my current NSF grant, in which we integrate ecology, phylogeny, taxonomy, and floristics both to expand our understanding of biodiversity and to achieve specific conservation goals. At the Mycological Society of America conference at Yale University, I organized a symposium on phylogenetic, ecological, and functional diversity of fungi. It was a great symposium, with an award-winning student talk given by Kathryn Picard! I also had a great time playing music with other conference attendees. I can't wait to see everyone again next year!

- Brendan