Bora Zivkovic's blog

Viruses in the Oceans: join the latest Journal Club

Bora Zivkovic — Wed, 20 Feb 2008 03:58:18 -0800

Brendan Bohannan, Richard W. Castenholz, Jessica Green and their students and postdcos at the Center for Ecology and Evolutionary Biology at University of Oregon are currently doing a Journal Club on the PLoS ONE article The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples, which is part of the PLoS Global Ocean Sampling Collection. Please join in the discussion.

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Open Students

Bora Zivkovic — Tue, 5 Feb 2008 18:33:28 -0800

Open Students is a new blog for students about open access to research. It is run by Gavin Baker (who also recently joined Peter Suber at Open Access News - Congratulations!) and sponsored by SPARC, the Scholarly Publishing and Academic Resources Coalition, as part of its student outreach activities.

The blog will cover the issues of Open Science as it affects the college students and will have frequent guest-bloggers (students, librarians, researchers, publishers...) - of which you can be one if you contact Gavin.

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PLoS Blog update

Bora Zivkovic — Tue, 22 Jan 2008 10:55:05 -0800

Last week, we made a little upgrade to the PLoS Blog.

If you look at any individual post you will see that we added the "e-mail this page" and "Printer-friendly version" buttons on the bottom of each post.

We have also started allowing trackbacks on our posts. Just like comments, trackbacks will be moderated due to large amounts of spam that are still attacking our system. We check the approval cue for comments and trackbacks on the blog regularly, so yours will show up after a short lag (and if it does not, give me a heads-up by e-mail).

Now look at the right side-bar, where we have made some re-arrangements, some features got new names, and new features have been added.

We have added a new Channel - In The News - where we will highlight the media and blog coverage of our most popular articles.

We have added a Technorati widget so you can see who links to the blog.

Finally, we also added the Blogroll. At the moment, the front page will showcase five from our very long list of favorite blogs and we'll rotate them to eventually give them all their time in the sun. If you want to make suggestions for our list you can let me know.

This is just the first set of small changes on the PLoS Blog. Keep an eye on it as more changes will be coming in the future, making the blog better, prettier and easier to use.

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New Journal Club!

Bora Zivkovic — Thu, 10 Jan 2008 21:13:27 -0800

Members of the Rodriguez lab and the Otero lab, both of Instituto de Neurociencias de Alicante (CSIC-Universidad Miguel Hernandez. Spain) have just posted their first Journal Club commentary on the PLoS ONE article High-Pass Filtering of Input Signals by the Ih Current in a Non-Spiking Neuron, the Retinal Rod Bipolar Cell.

Check their discussion and join in - respond to their comments or post your own discussions, annotations and ratings and keep the conversation going!

Also, it is never too late to add your thoughts to the previous Journal Clubs.

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Nigersaurus - the Media response

Bora Zivkovic — Mon, 19 Nov 2007 16:07:22 -0800

Last week's PLoS ONE article Structural Extremes in a Cretaceous Dinosaur has received a huge and positive response by the news media and bloggers. The story was featured on the radio, on NPR's Morning Edition ('Mesozoic Cow' Rises from the Sahara Desert) and on television, on ABC's Good Morning America.

As of this writing, Google has registered 583 news reports and 1,855 blog posts about Nigersaurus (only three of which, unfortunately, were trackbacked to the article itself). Under the fold is a choice collection of links to some of the most interesting reports and blog posts, but this should not stop you from adding your ratings, discussions and annotations to the article itself.

Media

New York Times: A Dinosaur That Grazed Like a Cow
Chicago Tribune: U. of C. scientist unveils skeleton of plant-eating dinosaur
LA Times: 'Cows of the Mesozoic' era discovered
Reuters: Weird dinosaur was 'cow of the Mesozoic': report
The Associated Press: Dinosaur Found With Vacuum-Cleaner Mouth
Pravda: Scientists discover dinosaur with vacuum cleaner-shaped mouth
TIME: Hoover-Mouthed Dino Discovered
Boston Globe: Herbivore dinosaur grazed like a cow
BBC: New type of dinosaur is unveiled
The Times: Big munch of the 30ft living lawnmower
Houston Chronicle: Long necks didn't all reach for the trees
Raleigh News & Observer: Dinosaur had mouth like a vacuum cleaner
Kalamazoo Gazette: Dinosaur hunter has deep roots in Kalamazoo
derStandard.at: Dinosaurus bizarrus
EurekAlert: Dinosaur from Sahara ate like a 'mesozoic cow'
ScienceDaily: Dinosaur From Sahara Ate Like A 'Mesozoic Cow'
National Geographic: Dino With "Vacuum Mouth" Revealed
National Geographic: Bizarre Dinosaur Grazed Like a Cow, Study Says
eFluxMedia: CT Imaging Sheds Light on Saharan Nigersaurus taqueti
New Scientist: Odd-jawed dinosaur reveals bovine lifestyle
LiveScience: Toothy Dinosaur Mowed Earth Like Cow
University of Chicago News Office: Dinosaur from Sahara ate like a ‘Mesozoic cow’
Latest from the Ann Arbor News: Eureka! New dinosaur discovered
Africasia: Anatomically odd African dinosaur sucked up the greenery
MLive.com: U-M researchers had role in Nigersaurus puzzle
Newswise: Dinosaur from Sahara Ate Like a ‘Mesozoic Cow’ (press release)
Raw Story: Anatomically odd African dinosaur sucked up the greenery
Scientific Frontline: Dinosaur From Sahara Ate Like A ‘Mesozoic Cow’

Blogs

A Blog Around The Clock: Extreme Dinosaur: Nigersaurus, the Mesozoic Cow!
Laelaps: Nigersaurus taqueti!
Pharyngula: Nigersaurus, a Cretaceous hedge-trimmer
Pondering Pikaia: Nigersaurus: just when you thought you'd seen everything...
When Pigs Fly Returns: Lawnmowers of the Early Cretaceous
Microecos: Pod People
PLoS Blog: The Nigersaurus has landed
Panda's Thumb: Nigersaurus, a Cretaceous hedge-trimmer
Clioaudio: The Open Access Dinosaur
Effect Measure: Lightweight dinosaur, heavyweight publishing event
The Beagle Project Blog: Open access science publishing lands a big one
The Tree of Life: Open Access dinosaurs and way to go Paul Sereno
Business|bytes|genes|molecules: Dinosaurs come with Creative Commons licenses too
Self-designed Student: Nigersaurus...and a question...
Science After School: Youth Involved in New Dinosaur Discovery
The Great Beyond (Nature): Dinosaur of the Day: a ‘Flintstones lawnmower’
Wired Science: This Week in Dinosaurs: A Mesozoic Vacuum Cleaner, An Accidental Find
Popular Science Blog: Dinosaur That Munched Like a Cow
Nonoscience: Nigersaurus, the Open Access Dinosaur
Transcription Factor: Thanks, Bora!
Be openly accessible or be obscure: Nigersaurus, the OA dino
Pixelshot: Dinosaur build
Pixelshot: Nigersaurus - raising the bones!
Braving the Elements: Strange New Dinosaur

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Where does a fruitfly go when it goes out for a walk?

Bora Zivkovic — Tue, 30 Oct 2007 13:43:04 -0700

Last week's PLoS ONE paper, Analysis of the Trajectory of Drosophila melanogaster in a Circular Open Field Arena, is the subject of the newest Journal Club. It is an interesting methods paper, showing the way a camera and some sophisticated math can be used for a much more sophistocated analysis of animal behavior than it has traditionally been done.

The Journal Club this week is being led by Bjoern Brembs from the Institute of Biology - Neurobiology, Freie Universitat Berlin. You may be familiar with his name because Bjoern also writes a science blog

The group has now posted some initial commentary, in particular a list of questions. It is now up to YOU to go and add your voice to the Journal Club - answer the questions if you can, or ask new questions, or just post a brief comment.

Here is the abstract, and you go read the entire paper, rate, comment, annotate, blog about and send trackbacks:

Background

Obtaining a complete phenotypic characterization of a freely moving organism is a difficult task, yet such a description is desired in many neuroethological studies. Many metrics currently used in the literature to describe locomotor and exploratory behavior are typically based on average quantities or subjectively chosen spatial and temporal thresholds. All of these measures are relatively coarse-grained in the time domain. It is advantageous, however, to employ metrics based on the entire trajectory that an organism takes while exploring its environment.

Methodology/Principal Findings

To characterize the locomotor behavior of Drosophila melanogaster, we used a video tracking system to record the trajectory of a single fly walking in a circular open field arena. The fly was tracked for two hours. Here, we present techniques with which to analyze the motion of the fly in this paradigm, and we discuss the methods of calculation. The measures we introduce are based on spatial and temporal probability distributions and utilize the entire time-series trajectory of the fly, thus emphasizing the dynamic nature of locomotor behavior. Marginal and joint probability distributions of speed, position, segment duration, path curvature, and reorientation angle are examined and related to the observed behavior.

Conclusions/Significance

The measures discussed in this paper provide a detailed profile of the behavior of a single fly and highlight the interaction of the fly with the environment. Such measures may serve as useful tools in any behavioral study in which the movement of a fly is an important variable and can be incorporated easily into many setups, facilitating high-throughput phenotypic characterization.

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Journal Clubs - think of the future!

Bora Zivkovic — Mon, 15 Oct 2007 06:14:40 -0700

The recent return of Journal Clubs on PLoS ONE has been quite a success so far. People are watching from outside and they like what they see.

The first Journal Club article, on microbial metagenomics, has already, in just one week, gathered 3 ratings, each accompanied with a short comment, two trackbacks and 7 annotations and 4 discussions eliciting further 14 responses in the comment threads. The 13-comment-and-growing thread on the usefulness of the term 'Prokaryote' is quite exciting, showing that it is not so hard to comment on PLoS ONE after all, once you get over the initial reluctance. You should join in the conversation there right now!

If you encounter a technical problem, please contact the Webmaster so the glitch can be fixed promptly. For a brand-new software built in-house, TOPAZ is performing remarkably well, but glitches do sometimes happen. It is essential to report those to the Webmaster so the IT/Web team can fix them quickly and make the site better and better for all users as time goes on. Just like anything else in development, it needs feedback in order to improve over time. For the time being, I guess, compose in Notepad, WordPad or something similar before copying and pasting there. And thank you for your participation.

One thing to keep in mind is that a PLoS ONE article is not a blog post - the discussion is not over once the post goes off the front page. There is no such thing as going off the front page! The article is always there and the discussion can go on and on for years, reflecting the changes in understanding of the topic over longer periods of time.

Imagine if half a century ago there was Internet and there were Open Access journals with commenting capability like PLoS ONE. Now imagine if Watson and Crick published their paper on the DNA structure in such a journal. Now imagine logging in today and reading five decades of comments, ratings and annotations accumulated on the paper!!!! What a treasure-trove of information! You hire a new graduate student in molecular biology - or in history of science! - and the first assignment is to read all the commentary to that paper. There it is: all laid out - the complete history of molecular biology all in one spot, all the big names voicing their opinions, changing opinions over time, new papers getting published trackbacking back to the Watson-Crick paper and adding new information, debates flaring up and getting resolved, gossip now lost forever to history due to it being spoken at meetings, behind closed door or in hallways preserved forever for future students, historians and sociologists of science. What a fantastic resource to have!

Now imagine that every paper in history was like that (the first Darwin and Wallace letters to the Royal Society?!). Now realize that this is what you are doing by annotating PLoS ONE papers. It is not the matter so much of here-and-now as it is a contribution to a long-term assessment of the article, providing information to the future readers that you so wished someone left for you when you were reading other people's papers in grad school and beyond. Which paper is good and which erroneous (and thus not to be, embarrassingly, cited approvingly) will not be a secret lab lore any more transmitted from advisor to student in the privacy of the office or lab, but out there for everyone to know. Every time you check out a paper that is new to you, you also get all the information on what others think about it. Isn't that helpful, especially for students?

So, go forth and comment on papers in areas you are interested in. And if you are a member of a lab group, a graduate seminar, an honors class, or an AP Biology class, let me know if you would be interested in doing a Journal Club on one of the PLoS ONE papers in the future - a great exercise for you, nice exposure to your group, and a service to the scientific community of today and tomorrow.

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Viruses in the Oceans: join the latest Journal Club

from A Blog Around The Clock on Wed, 2008-02-20 04:55

Journal Clubs are back!

Bora Zivkovic — Tue, 2 Oct 2007 10:41:58 -0700

Journal Clubs are a popular feature on PLoS ONE papers. We had several of them in the spring. Now, after a brief summer break, we are launching the Journal Clubs again and intend to have them happen on a regular basis, perhaps as frequently as one per week.

In short, a lab group volunteers to discuss one of the more recent (or even upcoming, not yet published) PLoS ONE papers and to post their discussion as a series of comments, annotations and ratings on the paper itself, triggering a discussion within a broader scientific community.

The first group that will start our Fall series is the Bacterial Metagenomics group led by Dr.Jonathan Eisen at UC-Davis. They chose to discuss last week's ONE article Metagenomics of the Deep Mediterranean, a Warm Bathypelagic Habitat and have posted first several parts of their discussion. So, you should go and read the paper and what the Eisen group wrote about it, then join in the conversation - add your own commentary, including annotations and ratings to the article.

And if you and your group would like to do a Journal Club in the future, let us know - e-mail me at: Bora@plos.org

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Trackbacks are here!

Bora Zivkovic — Fri, 21 Sep 2007 08:45:21 -0700

Yesterday, PLoS ONE moved to the newest version of the TOPAZ platform. Rich Cave explains all the improvements that this move entails, including the citation download for articles, but one new feature that should really be exciting to bloggers are Trackbacks.

From now on, if you link to a PLoS ONE article in your post, that article will display a link back to your blog post (go to an article and look at the right side-bar, nested between the Discussions and Ratings). Thus, in addition to the conversation already going on in the commentary attached to the article itself, the readers will be able to access the responses from the blogosphere as well. And that should also bring additional traffic to the bloggers.

We have been testing the feature over the past 24 hours or so, but we need your input in order to refine and improve the Trackbacks feature.

First, for the time being, the link you use in your post has to be in the format of the full URL of the full text (i.e., not the shorter, DOI-only compression), so this is how it should look like (replace 0000000 with the actual number of the article):

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000000

Unfortunately, for the time being (and we are working on it), this shorter form of the URL will not work:

http://www.plosone.org/doi/pone.0000000

Likewise, links to other parts of the site, e.g., to the PDF of the article, will not generate trackbacks.

So far, it appears that Trackbacks are working automatically on Drupal and MoveableType, i.e., there is no need for manual trackbacks.

In Wordpress.com, it is necessary to type the trackback URL into the appropriate field in your posting form. The trackback URL is in this form:

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000000/trackback

At this moment, it appears that links from Blogger/Blogspot blogs do not generate Trackbacks, but we are working on it. Test it anyway and let us know if there is a "trick" we missed so far.

Also, please let us know how it works on other platforms (e.g., Typepad, RadioUserland, Blogsome, LiveJournal, etc.)

I am not 100% sure (so tell me if I am wrong), but links posted "under the fold" will also not generate a trackback.

Also, and this may differ between platforms, I am not sure that republishing a blog (or an individual post) will trigger trackbacks from links made before yesterday. Give it a test run and let me know, please.

You can give us feedback in the comments here, or by e-mail (Bora@plos.org), or by contacting the Webmaster on the PLoS ONE site.

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New and Exciting in PLoS ONE

from A Blog Around The Clock on Wed, 2008-05-07 05:33

There are 56 new articles published in PLoS ONE this week and it was hard to make the picks as this seems to be a very, very good week with lots of cool papers. Here are some of the...

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New Journal Club on PLoS ONE - Chimps exchange fruit for sex

from A Blog Around The Clock on Mon, 2008-01-21 13:09

A paper published back in September - Chimpanzees Share Forbidden Fruit by Hockings et al. is getting renewed attention these days. Rebecca Walton has compiled links to the recent media and blog coverage of the paper (including those by my...

Help make NIH-funded research findings freely available to everyone!

Bora Zivkovic — Wed, 12 Sep 2007 07:36:04 -0700

Back in July, the House of Representatives passed a bill that requires all the NIH-funded research to be made freely available to the public within at most 12 months subsequent to publication.

The equivalent bill has passed the Senate Appropriations Committee earlier this summer and will be up for vote in the Senate very soon! In advance of this important vote, The Alliance for Taxpayer Access has issued a Call for action:

"As the Senate considers Appropriations measures for the 2008 fiscal year this fall, please take a moment to remind your Senators of your strong support for public access to publicly funded research and – specifically – ensuring the success of the National Institutes of Health (NIH) Public Access Policy by making deposit mandatory for researchers.

Earlier this summer, the House of Representatives passed legislation with language that directs the NIH to make this change (http://www.taxpayeraccess.org/media/release07-0720.html). The Senate Appropriations Committee approved a similar measure (http://www.taxpayeraccess.org/media/release07-0628.html). Now, as the Appropriations process moves forward, it is critically important that our Senators are reminded of the breadth and depth of support for enhanced public access to the results of NIH-funded research. Please take a moment to weigh in with your Senator now."

Read the rest for talking points and the contact information of your Senators, then do your part and contact them! And spread the word - by e-mail, posting on your blog or website, on forums and mailing lists. Let's get this bill passed this month and thus ensure that taxpayer-funded research is freely available to its funders - the taxpayers. This needs to be done no later than Friday, September 28, 2007, when the bill is slated to appear in the Senate.

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