PLOS
clock | August 7, 2008On Tuesday night, when I posted my personal picks from this week's crop of articles published in PLoS ONE, I omitted (due to a technical glitch on the site), to point out that a blog-friend of mine John Logsdon published his first PLoS ONE paper on that day:
It's a updated and detailed report on the ongoing work in my lab to generate and curate an "inventory" of genes involved in meiosis that are present across major eukaryotic lineages. This paper focuses on the protist, Trichomonas vaginalis, an organism not known to have a sexual phase in its life cycle.
Here is the paper (and check John's…
clock | August 4, 2008Two years ago on this day, PLoS ONE opened for submissions (and surprisingly many manuscripts - 70 - got submitted immediatelly).
clock | July 28, 2008For August, the theme is Natural and Synthetic Vision: Neuronal Mechanisms for Vision, Network Properties and Modeling, and Visual Psychophysics and Perception.
clock | July 25, 2008PLoS Genetics is celebrating its third birthday this month! Let's see what's new this week, among else...
PLoS Genetics Turns Three: Looking Back, Looking Ahead:
PLoS Genetics is three years old this month--a milestone worth celebrating! As we do, and as we recognize all who have helped us reach this point in time, we thought this would be a good opportunity to share with you a summary of our brief history and a look ahead.
Our original intent was to provide an open-access journal for the community that would "reflect the full breadth and interdisciplinary nature of genetics and genomics…
clock | July 17, 2008I am currently reading - and enjoying very much - The Carbon Age: How Life's Core Element Has Become Civilization's Greatest Threat by Eric Roston.
He was recently interviewed for DC Examiner and they ran a picture of him wearing a familiar t-shirt ;-)
Recently, Eric was quoted in TIME and lambasted by Rush Limbaugh, which, as Tom notes, means that Eric made it Big Time!
clock | July 17, 2008TOPAZ software, the one that hosts five out of seven PLoS journals (ONE, Pathogens, Neglected Tropical Diseases, Genetics and Computational Biology) has just been upgraded. There is not much new in the terms of functionality visible to readers, but the upgrade should greatly increase the stability of the sites and the speed of loading of papers, comments and other pages.
Give it a test-drive: search and browse papers, download PDFs, post comments/notes/ratings, send trackbacks, and if you notice any glitches, let us know exactly where you were, what you were trying to do, and what happened (…
clock | July 13, 2008Now that the spirited debate about the comparative business models of Nature and PLoS has died down, it is nice to take a little break from it all, and then start a new round - this time about publishing models, not business, and what it means for the future of the scientific paper - how the peer-review, impact factors, researcher evaluation, etc. are changing. Of course I am biased, but I love what Cameron Neylon just posted on his blog: What I missed on my holiday or Why I like refereeing for PLoS ONE:
To me the truly radical thing about PLoS ONE is that is has redefined the nature of peer…
clock | July 7, 2008As you probably know by now, we have monthly themes in PLoS ONE. This month, the topic is Gene Expression, where there are more than 140 articles already, mainly looking at genome-wide expression and epigenetics. Of course, we want more. And I am still looking for a group to do a Journal Club on one of the related papers, so if you are interested, let me know.
clock | July 3, 2008I know that you know that I work for PLoS. So, I know that a lot of you are waiting for me to respond, in some way, to the hatchet-job article by Declan Bucler published in Nature yesterday. Yes, Nature and PLoS are competitors in some sense of the word (though most individual people employed by the two organizations are friendly with each other, and even good personal friends), and this article is a salvo from one side aimed at another. Due to my own conflict of interest, and as PLoS has no intention to in any official way acknowledge the existence of this article (according to the old…
grrlscientist | July 2, 2008tags: researchblogging.org, open access, publishing, life science research, Declan Butler
Image: Orphan.
Wow, have you read Declan Butler's nasty little hatchet job that was just published in Nature about the Public Library of Science (PLoS)? My jaw hit the top of the table in my little coffee shop where I am ensconced -- why would Nature demean their journal by publishing such a snotty little screed where they attack the normal, but probably painful, financial ups-and-downs of a new journal?
Because Nature represents the old way of doing things, so Nature is afraid of those upstarts, PLoS…
clock | June 24, 2008As part of the monthly focus on birds, there is a new Journal Club in PLoS ONE this week.
Dr.Elizabeth Adkins Regan from Cornell and her postdoc Dr Joanna Rutkowska from Jagiellonian University have already posted their first comments on the paper by Keith Sockman (here at UNC): Ovulation Order Mediates a Trade-Off between Pre-Hatching and Post-Hatching Viability in an Altricial Bird.
You should all join in the discussion!
clock | June 18, 2008If anyone is interested, Thompson has just released the new Impact Factors for scientific journals. Mark Patterson takes a look at IFs for PLoS journals and puts them in cool-headed perspective.
One day, hopefully very soon, this will not be news. What I mean by it is that there soon will be better metrics - ways to evaluate individual articles and individual people in way that is transparent and useful and, hopefully, helps treat the "CNS Disease". Journals will probably have their own metrics based on the value they add, but those metrics will not affect individual researchers' careers…
clock | June 10, 2008If you are an astute watcher of the PLoS ONE homepage (or the PLoS Blog, or my blog for that matter), you may have noticed that PLoS ONE now has something like a 'theme of the month', i.e., a single, broad topic that we highlight in several different ways on the homepage, blog, in e-mails, etc. We check out the most viewed and downloaded papers on the topic and interview the authors and Academic Editors of those papers, etc. Last month, in May, the theme was Cell Signaling. This month, June '08, the overarching theme is The Birds!
If you search PLoS ONE for bird + avian (keep clicking '…
clock | June 6, 2008As it grew too big, and the functionality was lacking, the PLoS Facebook group has been closed and moved to a PLoS Facebook page instead. Join in.
clock | June 5, 2008Recent discussions about potential use of downloads in place of other bibliometric measures (including Impact Factor) made us think. So, we took a look at PLoS ONE stats to see which papers are the most visited to date. The results are here - the most visited ONE paper is Ionizing Radiation Changes the Electronic Properties of Melanin and Enhances the Growth of Melanized Fungi, which got quite a lot of coverage in the media and on blogs (including BoingBoing, Slashdot, Rhosgobel, to point to just a few) when it first came out a year ago.
In second place is Paul Sereno's Structural Extremes…
clock | June 2, 2008First LOL PLoS images are now on Flickr and Facebook. If you use the correct tag in Flickr, yours will be added to the set. Please link to the original paper when you do this.
clock | May 30, 2008Kevin Zelnio and Alex Wild note that PLoS ONE published its first Taxonomy paper this week - A Revision of Malagasy Species of Anochetus Mayr and Odontomachus Latreille (Hymenoptera: Formicidae) by Brian Fisher and Alex Smith. Kevin explains the paper in detail and explains why this brave move by PLoS is good and important especially considering how many new species are discovered and described each year.
clock | May 29, 2008Every now and then I have some fun and LOL-cat-ize an image from a PLoS ONE paper. See, for instance, LOLdinosaur, LOLtortoise, LOLtasmaniantiger and LOLpterosaur. Folks at the mothership love these. So, if a number of you are up to this I'll make a Flickr set or Facebook group, or a linkfest. Pick your favourite PLoS papers, grab images, LOLcatize them (here) and send them to me, or give me the links. Ideally, if you post these on your blogs, provide also a link to the paper itself or at least let me know which paper they came from.
This is not what I have in mind, but it is a LOL and a…
awild | May 28, 2008
Odontomachus coquereli - Madagascar
Myrmecology continues to lead the way in online taxonomy. Today saw the release of the very first taxonomic paper published by the top-tier open access science journal, PLoS One.
Brian Fisher and Alex Smith combine alpha taxonomy with DNA barcoding to produce a revision of the Malagasy trap-jaw ants. The revision includes mitochondrial DNA sequences from some 500 individual ants and resulted in the inference of several new species. I've got plenty to say about DNA barcoding, but I'll leave that for a later post and instead point you to the thoughtful…
clock | May 25, 2008A couple of days have passed and I had a lot of work-related stuff to catch up with, but I thought I better write a recap now while the iron is still hot and I remember it all. Here we go....
Surprise #1 Last time I went to a SRBR meeting (or for that matter any scientific meeting) was in 2002. I started my first blog in 2004. I started writing about science, specifically about Chronobiology, in January of 2005.
Before last week's meeting I knew of one chronobiologist who reads my blog regularly. I knew of one other chronobiologist who contacted me to ask to use some of the material for…