Public Library of Science

New spring range now available in the PLoS Store

Liz Allen — Fri, 5 Feb 2010 10:29:46 -0800

When we launched the PLoS store back in November 2009, we promised to continually update it with new designs and merchandise. We've been true to our word. For the last couple of months, we've been creating our Spring range, so now you, your home, office or lab and the kids in your life can look cool and support the PLoS cause.

Over the years, folks have continually asked us for a Future PLoS Author kids range - you are never too young (or old) to get behind Open Access. As you can see from the adjacent photo of Pete and his daughter, we road tested these designs and products on our own kids. When we were told by the eloquent three year old of one of our team that she couldn't read the words on the tees because they were too fancy, we changed them so that they were readable.

For those of you who prefer a more classic look, there are new embroidered tees, hats and hoodies. We think these look particularly nice on a classic polo or baseball cap, but you can decide for yourself how and where (they are smart enough for the boardroom of golf course) you want to wear them.

Since everyone loves dinosaurs and PLoS ONE in particular publishes a large amount of Paleontology research, we couldn't resist developing a range around this theme. We have dino tees, mugs and mousepads, just take your pick.

While we were in all out creative overdrive, we also came up with new mug designs and a few posters to brighten your home or lab walls, so check them out.

Visit the PLoS store today to find these featured products and many more. Through your purchase, you can support our non-profit mission. Happy shopping!

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Details on Outage and Recovery of PLoS Journal Websites

Richard Cave — Wed, 20 Jan 2010 10:52:39 -0800

UnitedLayer, our collocation facility for the production servers, experienced an outage yesterday. From UnitedLayer: "A series of power brownouts occurred today at 2:56 PM PST due to PG&E instability related to the recent storms. Our 300KVA UPS system is not working as designed, the temporary repairs from last week did not hold. We anticipate a faulty motherboard."

A number of our servers (all powered by the 300KVA UPS) lost power at that time. Our large disk array (2TB of storage) that is the file server for both Fedora and Mulgara had a boot failure and refused to power up. Russ went to the colo and restarted the disk array which went into an automatic rebuild of the disks. This took about three hours to complete. Russ then started a program that checks for disk consistency and repairs any problems in the drives. This program was still running at 8pm – any recovery would have to wait until the program ended (many more hours). We made a decision to stop the program, format the drives and restore Fedora and Mulgara from a previous backup to speed up recovery.

We estimated that it would take ~3.5 hours to restore Fedora from backup. It took ~5.5 hours. Once complete, Russ brought the systems back online at ~2:50AM PST. Big thanks to Russ for babysitting the file server the whole day/night and for bringing up the system after the backups completed.

This is the first time that we had a major hardware malfunction to the large disk array and the first time we had to restore from a backup. While the disaster recovery plan worked, it took much longer than expected due to the size of the Fedora storage. We will look into solutions that enable a quicker disaster recovery. We are also meeting with UnitedLayer to discuss mitigation options.

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PLoS Journals Outage - January 19, 2010

Richard Cave — Tue, 19 Jan 2010 16:57:47 -0800

The PLoS journal websites are experiencing an outage due to a hardware malfunction after our colocation (United Layer) experienced a brown out due to lightning. We're working to resolve the problem and hope to have the journal websites back online soon.

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Announcing a new PLoS Collection, Tagging of Pacific Predators (TOPP)

Liz Allen — Thu, 14 Jan 2010 14:00:14 -0800

Today, PLoS is delighted to publish a Collection of articles highlighting biologging research from the Tagging of Pacific Predators group (TOPP), a Census of Marine Life (COML) project.

Advances in electronic marine tracking technology, also known as biologging, allow researchers to take measurements from free-swimming marine animals as they move undisturbed through their environment. Recent technology improvements, including electronic tag miniaturization and enhanced animal movement models, have revolutionized understanding of the ecology of marine top predators. This has permitted observations well beyond the reach of standard measurement techniques, and provided extensive data on the animals' behavior at the scale of and within the context of their environment. Such studies are essential for the effective management of marine ecosystems and conservation of top predator populations.

The first six articles (five from PLoS ONE and one from PLoS Biology) to be published in this Collection have examined how our understanding of animal movement and migration has been improved by electronic tagging and tracking across a diverse range of marine species including sharks, tunas, sea birds, sea turtles and marine mammals. More work will be added to this "living" collection as soon as each TOPP article is published.

In the coming months, PLoS will be publishing more Biodiversity research from other groups that make up the Census of Marine Life, a 10 year project to explore and understand the diversity and distribution of life in the oceans, past, present and future. In this so called "transparent ocean" scientists will have the tools to say where marine organisms are, how many of them there are and where they are going - knowledge which will help mankind best conserve and support these precious resources.

Here's what Dr Randy Kochevar, TOPP Marine Biologist and Science Communicator, said about his experience of working with PLoS on this collection: "TOPP is a broad, interdisciplinary program - and it's fantastic to have a range of articles represented in this PLoS collection, freely accessible online to the world thanks to open-access publishing. We are excited about the media coverage this exposure has brought us and we look forward to adding to the collection in the future – we would encourage other groups within the COML community to publish their work in PLoS ONE. They really are a pleasure to work with.”

Other member groups of COML who also want to work with PLoS to create a collection are encouraged to contact Pete Binfield (pbinfield@plos.org), the Publisher of PLoS ONE and the Community Journals for more information.

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PLoS ONE indexed by Web of Science

Mark Patterson — Tue, 5 Jan 2010 12:16:28 -0800

Today we learned that by the end of this week PLoS ONE (in keeping with all other PLoS journals) will be indexed by the Web of Science – this is an important literature discovery tool that many people use and so we are pleased to be indexed. PLoS ONE is also indexed by a host of other services such as PubMed, MEDLINE, PubMed Central, Scopus, Google Scholar, the Chemical Abstracts Service (CAS), EMBASE, AGRICOLA, PsycINFO, Zoological Records, FSTA (Food Science and Technology Abstracts), GeoRef, and RefAware.

Initially, coverage in the Web of Science will include new PLoS ONE articles plus those published in 2008 and 2009, and will be expanded to the articles published in 2006 (when PLoS ONE was launched) and 2007 in the coming weeks. Inclusion in the Web of Science also means that in June 2010 PLoS ONE will receive journal-level citation data from Thomson Reuters including a 2- and 5-year Impact Factor and Eigenfactor metrics.

As we have previously indicated, PLoS believes that research articles are best assessed on their own merits, rather than on the basis of the journal (and its impact factor) where the work happens to be published. While we are happy that PLoS ONE articles will become more discoverable as a result of their inclusion in the Web of Science, we will continue to push forward with our Article-Level Metrics program.

Naturally, we understand that inclusion in the Web of Science is significant for many academics whose research output is still measured by traditional means. We hope that this news encourages even more scientists to publish their work in PLoS journals, to benefit from the article-level metrics that are provided for every PLoS article (for example, this PLoS ONE article), and to ensure that all interested users have open access to their research.

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PLoS Author Surveys 2009 – Summary Presentation

Mark Patterson — Wed, 23 Dec 2009 02:45:25 -0800

Earlier this year, PLoS sent out a series of surveys to authors whose work was considered by our journals in 2008. We wanted to find out what authors think about all aspects of our services – from submission and peer review, through to publication and the functionality of the PLoS journal web sites.

We have learned a lot from the surveys, primarily that levels of satisfaction amongst authors are generally very good. We also identified areas where services can be improved, and we’ve adjusted our services in a number ways during 2009.

We have now summarized the results of the surveys along with how we have responded to some of the suggestions during 2009 in a short presentation, which is publicly available. We feel it’s important to share these results in particular with the authors who were kind enough to complete the questionnaires, and we would like to express our thanks to the hundreds of authors who took part. We are planning to repeat the surveys next year, so that we can monitor how views have changed and can respond to suggestions for further improvements.

Meanwhile, we welcome feedback from anyone who is using our services, as an author, reviewer, editor or reader.

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New addition to Article-Level Metrics - blog posts from ResearchBlogging.org

Liz Allen — Thu, 17 Dec 2009 11:19:50 -0800

Throughout the course of 2009, PLoS has been adding a range of Metrics to each and every article that it has published. In addition to the many metrics already displayed (article pageviews and downloads, citations, social bookmarks, notes, comments and ratings), we are pleased to now add data relating to the blog coverage of any article, as measured by ResearchBlogging.org. You can find out more about the Article Level Metrics program here.

Every interested author and user can now see how many times an article has been downloaded (split into HTML Pageviews, PDF and XML downloads and displayed in a month-by-month format); how often an article has been cited (as measured by PubMed Central, Scopus and CrossRef); how many times it has been ‘socially bookmarked’ (at CiteULike and Connotea); how many times users have Commented, or left Notes, or provided Ratings; and how many blog articles have been written about it (as measured by the blog aggragators Postgenomic, Blog Lines, Nature Blogs and, from today, ResearchBlogging.org).

We've created a 2.4 minute screen shot video (with audio commentary) that you can watch to familiarize yourself with the blog aggregation functionality from ResearchBlogging.org so you can see for yourself the benefits of this part of the Article-Level Metrics program.

On launching this new functionality, Pete Binfield, Publisher of PLoS ONE and the Community Journals said:

"We're delighted to add data from ResearchBlogging.org to the Article Level Metrics program because the blogs that they index are mainly written by practicing scientists, who are well versed at providing readable summaries of the research that we publish".

Bloggers who regularly write about scientific research are able to register with ResearchBlogging.org and (provided they qualify) they are then entitled to indicate that their blog entries refer to peer reviewed scientific research by adding an icon to their posts. As a result, the ResarchBlogging.org service represents a high quality source of highly relevant articles, typically written by practicing scientists, on the topic of peer reviewed research. Since all PLoS content is peer reviewed and free to read, PLoS articles tend to be regularly covered by their bloggers. You can find the current list of qualified ResearchBlogging.org bloggers here.

Dave Munger, the co-founder of ResearchBlogging.org, said:

"We’re pleased to be working with PLoS to assess the impact of its articles. PLoS journals do a great job publishing and making research accessible to everyone, and we think coverage in thoughtful blog posts is an important component of the impact of a peer-reviewed journal article". You can read more in this blog post.

PLoS ONE and ResearchBlogging.org also collaborate on a monthly "Blog Pick of the Month" competition that we feature on everyONE, the PLoS ONE community blog. Every month, Bora Zivkovic, the Online Discussion Expert for PLoS, chooses the best blog about a PLoS ONE article that has appeared in ResearchBlogging.org and we feature it on our blog. The winning blogger and all the authors of the original PLoS ONE research article all win t-shirts. To enter, you simply need to be a ResearchBlogging.org blogger and start writing about PLoS ONE articles.

We welcome feedback and questions on any aspect of this program to alm@plos.org.

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Update of the PLoS Journals to Ambra 0.9.5

Richard Cave — Wed, 16 Dec 2009 16:45:54 -0800

We will update the PLoS journals with the Ambra 0.9.5 release tonight. This release focused on development of the long-awaited PLoS Queue syndication module. Starting in January, PLoS will send article packages directly to PubMed Central at publication time. Article packages are currently sent to PubMed Central the same time as they arrive at PLoS so if any errors are found by the PLoS editorial or production teams, we need to send the fixed article packages back for revision. Sending these article packages at publication time will save a lot of time/effort if any errors are found. This also allows us to automatically send article packages, XML and PDFs to other external repositories in the future. The admin panel and publication workflow were updated for this new syndication service.

New features and updates:

Added a new syndication service to the Admin panel. This will allow administrators to export article files and metadata to external sources. PLoS is using this syndication service with an internal application built on Apache Camel to send published files to PubMed Central and other external repositories. This is not an out-of-the-box solution as only the service hooks are available in Ambra.
Added RDFa for the Dublin Core elements in the article HTML. Look for a blog posting on this feature soon!
Added a new action to support a Google Scholar XML feed for published articles.
Update to the article RHC to display articles cross-published in other journals.
Improvements to how XSL sheets are configured.
Upgraded the Dojo library to 1.3.2.

Bug fixes:

Promote a note to a formal correction and the annotation body was removed.
Templates from other journals were displayed if freemarker.properties template_update_delay was set.
Templates changes to fix a number of formatting errors encountered in IE6, IE7 and IE8.
Minor fixes to annotation displays, formal corrections, formatting and messaging.

For a complete list of 0.9.5 features and bug fixes, please see the Ambra 0.9.5 RC1 Tickets and the Ambra 0.9.5 RC2 Tickets.

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Be heard at the White House - tell them why you support public access to research

Liz Allen — Wed, 16 Dec 2009 10:43:12 -0800

The White House Office of Science and Technology Policy has invited comment on broadening public access to publicly funded research and they want to hear from you. Please post your contributions to this blog.

Their Request for Information (RFI) lasts for just 30 days and expires on 7 January 2010, so we'd like to encourage you to get involved sooner rather than later. This is an opportunity for us to shape a broader public access policy - how it should be implemented, what type of technology and features are needed, and how to manage it.

Adding your thoughts to the blog will help ensure that the administration form a balanced (the comment thread is moderated) view of stakeholders' interest. E-mail comments will also be accepted and will be posted to the blog by the moderators.

There are 3 main topics where the administration would appreciate your input (they also welcome general comments) and each one is open for a set period of time:

1. Implementation - expires 20 December 2009. Which Federal agencies are good candidates to adopt Public Access policies? What variables (field of science, proportion of research funded by public or private entities, etc.) should affect how public access is implemented at various agencies, including the maximum length of time between publication and public release?

2. Features and Technology - 21-31 December 2009. In what format should the data be submitted in order to make it easy to search and retrieve information, and to make it easy for others to link to it? Are there existing digital standards for archiving and interoperability to maximize public benefit? How are these anticipated to change?

3. Management - 1-7 January 2010. What are the best mechanisms to ensure compliance? What would be the best metrics of success? What are the best examples of usability in the private sector (both domestic and international)? Should those who access papers be given the opportunity to comment or provide feedback?

Thanks for supporting this initiative.

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Just 3 more days to shop the PLoS Store and get your gifts by Christmas - free shipping available

Liz Allen — Tue, 15 Dec 2009 14:03:02 -0800

The holiday season may be in full swing but here at PLoS we're so busy stimulating debate over at the White House about public access to research and releasing new technology upgrades, that we don't have much time to do our shopping.

If you are in a similar situation and would like to support us, you'll be delighted to know that for the next 3 days you can still shop the PLoS store and get your goodies in time for Christmas. We even have a specially designed holiday range should you wish to really get into the festive spirit.

And, what's even better is that ground shipping is free on orders over $50. Outside the US, there's 50% off express shipping at the moment. It's also worth remembering to visit our local stores in the UK, Germany, Australia, Canada and New Zealand and now also in Spain, France, Brazil and Portugal. if you live in those countries, shopping locally always gives faster delivery and lower costs.

But these offers won't last, in the US you'll be too late by 3pm PT 12/17 and outside the US, it looks like you have one extra day, until 12/18.

So get your skates on and glide on over to our store today.

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