PLoS Director of Publishing moves to new OA initiative

By Peter Jerram
Posted: October 10, 2011

The Wellcome Trust, Howard Hughes Medical Institute and Max Planck Society have announced today that Mark Patterson (PLoS Director of Publishing) will be joining Randy Schekman (Professor of Cell and Developmental Biology, University of California at Berkeley) to lead the creation of a new high-profile open-access biomedical research journal to be launched in 2012.

We’re saddened that Mark will be moving on from PLoS, and at the same time delighted to see him move on to such an important open-access project.  As a founding member of PLoS, Mark has achieved a great deal over the past eight years.  He has been instrumental in establishing PLoS as a world leader in open-access publishing and has helped us to launch journals as well as initiatives in research communication that consistently break new ground.

Mark’s also represented PLoS and open access more broadly in a number of different ways, for example by helping to found the Open Access Scholarly Publishers Association.

On the new project, Mark said “This new journal, sponsored by three of the world’s leading funding agencies, has the potential to be a tremendous positive force for change in research communication and will drive forward open access to all research outputs.” and added that “Of course, it’s very hard to leave PLoS after so long, but the organization has never been stronger than it is today.”

We wish Mark, Randy and the new open-access publishing project all the success in the world, and are looking forward to future collaborations.

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DIY Science at #SciBarSpace 2

By Stacy Konkiel
Posted: August 30, 2011
Brian Mossop introduces Jason Bobe at #SciBarSpace, August 24, 2011

Brian Mossop introduces Jason Bobe at #SciBarSpace, August 24, 2011

Citizen scientist and co-founder of DIYbio.org, Jason Bobe, gave a lively presentation on amateur science initiatives at the 2nd #SciBarSpace event last Wednesday, August 24th, at PLoS’s San Francisco office. Below you’ll find our photo highlights and a recap of the event as archived on Storify by our Community Manager, Brian Mossop.

Many thanks to all those who attended, as well as to Jason Bobe, for helping to make this event a success!

Our second #SciBarSpace event was as well attended as the first, with over 60 guests in attendance

Our second #SciBarSpace event was as well attended as the first, with over 60 guests in attendance

Jason Bobe and Peter Binfield chat at #scibarspace, August 24, 2011

Jason Bobe and Peter Binfield chat at #SciBarSpace, August 24, 2011

Jason Bobe explains his project Bioweathermap.org to the crowd at #SciBarSpace

Jason Bobe explains his project Bioweathermap.org to the crowd at #SciBarSpace

Bobe recounts how he swabbed dollar bills for the Bioweathermap project to track "microbial weatherfronts."

Bobe recounts how he swabbed many dollar bills (including Jonathan Eisen's) for the Bioweathermap project to track "microbial weather fronts"

Read on for highlights of the event by Brian Mossop and the science Twitterati:

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App Ideas Announced – Develop One for the Binary Battle!

By Stacy Konkiel
Posted: August 18, 2011

Just eight days after announcing our call for App ideas, we received over 70 top-rate suggestions for scientific and medical apps from our community. Many addressed issues already important to PLoS—post-publication peer review and contextualizing and filtering research for a variety of disciplines. Others submitted ideas that were just plain cool but outside of the scope of the Binary Battle competition.

Now we are passing these ideas along to members of the developer community, who have the coding skills to bring them to life.

Below, we have broken these ideas into two groups:

  • Ideas that can use the PLoS or Mendeley APIs and can be entered into the Binary Battle competition
  • Cool ideas that don’t use the PLoS or Mendeley APIs (and are therefore outside of the scope of this competition) but you might want to tinker with anyway.

Selected Binary Battle-eligible ideas include:

  • An app for displaying the impact of diverse research outputs on your CV or website. For example, how many blogs have written about your paper, how often have your datasets been mentioned in scientific lit, etc. An existing app that does just that, called Total Impact but it needs to be taken from prototype to full-fledged app. More info here and here. Suggested by Heather Piwowar: hpiwowar(at)gmail(dot)com or total-impact(at)googlegroups(dot)com
  • Create an easily embeddable, dynamically-updating list of PLoS or Mendeley papers from a particular lab or institution that researchers can put on their websites. Suggested by Sébastien M. Crouze:  seb(dot)crouzet(at)gmail(dot)com
  • From a bunch of papers, recursively extract all the references they contain and establish a ranking of the most cited papers. It will help to found “must read” papers from a certain website, subject area, author(s), or institutions. Suggested by anonymous.
  • Search papers in Mendeley or PLoS based on geography or genes. Suggested by Sjurdur Hammer:  sjurdur(at)hotmail(dot)com and anonymous, respectively
  • A tool that will automatically export illustrations and figures (as well as their attributions and CC licenses) from PLoS papers to the Wikimedia Commons. Suggested by anonymous.
  • More ideas here

Other cool ideas

  • A searchable directory that could collate grant/funding opportunities from across all Federal, State and Foundation entities that are currently silo-ed into individual, closed databases on individual websites. This master databank should then be sortable by field, interest area, investigators (e.g. young investigators, tenure-track faculty, postdoc, etc.), funding amount, etc. Suggested by Llewellyn Cox, PhD:  llewellc(at)usc(dot)edu
  • A citizen science measurement app (like NYC Cricket Crawl) via GPS, photo, video, audio recording that sends data in standardized format. Suggested by mik3cap.
  • An app for identifying bat species from the sounds they make. You would hold up the smartphone and it would record a sound and then give you a species identification on the phone. Suggested by Dr. Kate Jones: kate(dot)jones(at)ioz(dot)ac(dot)uk
  • An educational App which finds the most recent common ancestor between any two species on the planet. Suggested by aulridgejr(at)gmail(dot)com
  • More ideas here

To sign up to develop an idea or request an API key from PLoS or Mendeley, fill out this form. We encourage you to work with other devs who share an interest in the idea you choose, and also to contact the scientist who conceived of the idea, should you seek more input or wish to invite them to collaborate.

Finished apps for the Binary Battle competition must be received by September 30th. Tim O’Reilly looks forward to seeing your creations – happy coding!

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Category: App competition, General, Publishing, Technology | 4 Comments

PLoS Currents: Muscular Dystrophy – open for submissions

By Liz Allen
Posted: August 9, 2011

We’re pleased to announce that another new section of PLoS Currents, on the topic of Muscular Dystrophy, is open for submissions.

We invited Dominic Wells (Professor in Translational Medicine, Royal Veterinary College, London) from our editorial board to share his thoughts about this important new site and his reasons for taking part. Below he issues a challenge to this research community to use this new forum to increase the speed of advances in the understanding and treatment of DMD and related muscular dystrophies.

“I am delighted to have been asked to act as one of the Editors of PLoS Currents: Muscular Dystrophy. This is a new forum, produced with support from Parent Project Muscular Dystrophy, for the rapid communication of hypotheses and experimental results.

The attractive elements of this publishing approach are obvious: publication will be rapid (the aim is to achieve a one week turnaround and ideally as fast as 24 hours); manuscript preparation will be simple (currently using the Google Knol web based platform); quality will be assured by a panel of internationally recognized reviewers; articles will be date-stamped, citable and immediately indexed in PubMed; unlike print and other web-based journals there will be no page charges and all content will be open access. Contributions can be updated and a trail of previous versions will be archived.

I suspect like many other potential authors, I had concerns when initially presented with this idea. Would this result in the publication of poor quality science and would people publish in a forum that did not have an impact factor, given the undue importance placed on the latter by promotion boards and funding agencies? After careful consideration, I believe these are not major problems. Given the light touch peer review system the published work should be seen as preliminary although we will take care to check there are no obvious methodological errors, ethical or legal concerns. Publication in PLoS Currents: Muscular Dystrophy will not bar a more complete or definitive version of the work from being published later in other members of the PLoS family of journals and possibly other long-established journals.

What type of content will be suitable for PLoS Currents: Muscular Dystrophy? The main criteria will be that the work is clearly related to Duchenne Muscular Dystrophy (DMD) and associated disorders that affect similar cellular processes. I expect a wide range of contributions from complete and comprehensive manuscripts through to interesting preliminary experiments; from exciting advances in potential therapies to no less important “negative” results; and from hypotheses to improved methodology. As a consequence, this will prevent a number of different laboratories repeating the same unsuccessful work, will generate an increased set of experimental data from which to develop new ideas and will allow the rapid spread of improved techniques and testable hypotheses.

I take this opportunity to challenge the muscular dystrophy research community to use this forum to increase the speed of advances in our understanding and treatment of DMD and related muscular dystrophies”.

PLoS Currents: Muscular Dystrophy is currently accepting submissions, please see the Author Guide and you are welcome to email your questions or submissions.

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Category: PLoS Currents | 1 Comment

Call for Scientific App Ideas

By Stacy Konkiel
Posted: August 2, 2011

Have a great idea for a scientific app but lack the coding skills to develop it? We’d like to hear it!

Submit your app idea by August 10th (12pm PDT) and we’ll present it to the developer community, who have the skills to make your dream app a reality. Ten (10) randomly selected winners will receive a PLoS t-shirt (Terms and Conditions apply).

Apps will be created by mining PLoS and Mendeley APIs and will have the potential to make your life easier and science more open.  Here are just a few of the possibilities:

  • Mine PLoS articles for statistically relevant words or phrases using the Solr API
  • See how many people are reading your papers and how you compare to other researchers on Mendeley with ReaderMeter
  • Determine the top papers read by researchers in particular subject areas in both  Mendeley and the PLoS journal family

How To Submit Your App Idea:

  • Complete the form at the Binary Battle App Idea Submission site [UPDATE: Now closed!] OR
  • Tweet your idea with the hashtag “#binarybattle” OR 
  • Leave a comment on this blog post with your idea and an email address

If you’re a developer, you may wish to enter your completed app into the Binary Battle by September 30th, 2011.

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Category: Alt-Metrics, App competition, Social media, Technology | 6 Comments

Final call for Conference Postcards from Vienna

By Cecy Marden
Posted: August 1, 2011

If you attended ISMB/ECCB 2011 and you’re planning to send PLoS Computational Biology a Conference Postcard then act now! We’ve heard from some of you but the deadline for submissions is August 2nd, and we want your perspective on the highlights of the conference, so email your Postcard to contribute[at]plos.org.

Please remember that your Conference Postcard should be between 800-1000 words, and should include:

o A synopsis of what was presented.

o Reasons why you think your chosen highlight is outstanding.

o How it related to the theme of the meeting.

o The impact it had on attendees.

o Additional references considered useful.

You can find full information regarding what is needed and who has given their agreement for their session/talk/workshop to be written about on the ISMB website: http://www.iscb.org/ismbeccb2011-program/plos-postcards.

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PLoS Article-Level Metrics API launched

By Liz Allen
Posted: July 27, 2011

We’re pleased to announce the launch of the Article-Level Metrics API. This Application Programming Interface (API) gives developers access to the statistics (usage, citations, social bookmarks, comments, notes and ratings) that have been on every PLoS article since March 2009 – allowing the community to measure the impact of research in the digital age.

This API provides those who want to enter the PLoS/Mendeley Binary Battle an additional data source to use along with the PLoS Search API.

We also have an open-source article-level metrics project site for other publishers who want to build on what we started and use this code on their own statistics. Publishers who have questions about using the code on their own journals should email Pete Binfield, Publisher of PLoS ONE and the Community Journals.

Here’s what Rich Cave, PLoS Director of IT, said about this development: “Releasing our ALM code base is a natural extension of our open philosophy. Not only are all our open-access articles freely available online but the tools that we use to add value to them are open-source.”

For those who follow our Article-Level Metrics project, it’s worth noting that we’ve also added PubMed Central usage statistics including the number of unique views and PDF downloads.

We hope that today’s announcement will provide the community with a powerful new way to leverage our content and their own and provide more reasons for developers to enter the PLoS/Mendeley Binary Battle.

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2010 PLoS Progress Update

By Peter Jerram
Posted: July 20, 2011

Today, PLoS released our 2010 Progress Update which, in addition to summarizing the year’s developments, reports that we covered our operating costs with revenue for the first time–-adding to the growing body of evidence that high-quality open-access publishing is sustainable. We’re also pleased to announce that for the second consecutive year our publication fees will not increase.

Vital to our success over the years has been the tremendous support of the Board of Directors (current and former members) and the broad community of stakeholders who are driving open access to research: the Gordon and Betty Moore Foundation and the Sandler Foundation provided the funding that launched PLoS; the many research funders who have developed policies that support open access publishing; the libraries and institutions which have shown unrelenting commitment to open access; and the tens of thousands of researchers who have demonstrated their belief in open access as authors, reviewers and editorial board members of PLoS journals.  Our thanks to everyone involved, and especially to the people at PLoS who have worked so hard to make all this possible.

We look forward to demonstrating not just how open-access publishing can work, but also how creative use of online tools and digital media in innovative projects like PLoS Hubs, PLoS Currents and Article-Level Metrics can drive a fundamental transformation to more open and effective research communication.

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Category: Progress Update | Tagged | 3 Comments

PLoS ONE Wins Recognition as a “SPARC Innovator”

By Stacy Konkiel
Posted: June 30, 2011

“For blazing a new trail in open-access journals, inspiring broader change in scholarly publishing, and thriving along the way, SPARC (the Scholarly Publishing and Academic Resources Coalition) has named the Public Library of Science’s (PLoS) PLoS ONE as the SPARC Innovator for June 2011.”

Today it was announced that PLoS ONE has been named a SPARC Innovator by the Association of Research Libraries’ Scholarly Publishing and Academic Resources Coalition. We are very proud to have received this significant honor from a leading resource in Open Access (OA) advocacy.

In particular, SPARC’s recognition of PLoS ONE (which you can read in full on the SPARC website) highlights our contributions to changing the way science is communicated (namely, post-publication peer review and alt-metrics) and our success in proving that Open Access publishing is a viable and successful business model.

“PLoS ONE is a game-changer. It breaks through the preconception that authors—and readers—require a journal to determine the significance of scientific research, and demonstrates that the community is ready and willing to take on that role,” says Heather Joseph, SPARC’s Executive Director.

In welcoming this award, we also want to highlight the fact that our tremendous success has been made possible thanks to the dedication of our staff, authors, editors, reviewers and everyone in the PLoS ONE ecosystem. This award and others are for them.

This announcement has been cross-posted from the everyONE blog.

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Category: PLoS ONE, Publishing | 1 Comment

Conference Postcards from Vienna

By Cecy Marden
Posted: June 30, 2011

PLoS Computational Biology invites you to send us a postcard from ISMB/ECCB 2011 ! PLoS Conference Postcards represent a novel way for upcoming members of the scientific community to report on cutting-edge research presented at key conferences. Your Postcard will focus on one of the highlights of ISMB – a keynote, paper presentation, poster session, software demonstration, or tutorial. All Postcards will be considered by the Editors and those selected will be published in PLoS Computational Biology as part of an article summarizing the conference.

Your Conference Postcard should be between 800-1000 words, and should include:

o A synopsis of what was presented.

o Reasons why you think your chosen highlight is outstanding.

o How it related to the theme of the meeting.

o The impact it had on attendees.

o Additional references considered useful.

Preference will be given to reports that demonstrate evidence of additional research into the topic. No permission from speakers is required beyond those obtained by ISMB.

Please find full guidelines on the ISMB website.

Send your submission to contribute[at]plos.org by August 2nd

Need inspiration? Check out previous Postcards articles at our new collection.

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