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Research Article

PLOS Journals Sandbox: A Place to Learn and Play

  • Mike Baehr,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Sarah Burt,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • John Callaway,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Richard Cave,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • John Chodacki,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Eddie Dickey,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Jonas Dupuich,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • James Harney,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Yesica Hurd,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Jennifer Lin,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Nina Meechoonuk,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Bill O'Connor,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Joe Osowski,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Juan Peralta,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Patrick Polischuk,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Rajani Samidi,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Lisa Siegel,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Mamta Singh,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Ryan Skonnord,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Jennifer Song,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Sebastian Toomey,

    Affiliation: Public Library of Science, Product Team San Francisco, California, United States of America

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  • Srujana Tumu,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Jackie Yao,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Michael Walsh,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Jack LaBarba,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Matt Bowen,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Jeffrey Gray,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Jonathan "Jono" Finger,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Holly Allen mail,

    To whom correspondence should be addressed. E-mail:webmaster@plos.org

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Eric Lopatin,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Kyle Pang,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Fernando Cabrales,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Polina Grinbaum,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • John Bertrand,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Sahar Aghajani,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Angela Melkisethian,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Anne Tran,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Christina Von Raesfeld,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Daniel Linsteadt,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

    X
  • Emma Dupin,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

    X
  • Helen Atkins,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

    X
  • Kevin Brandt,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

    X
  • Yanwu Zhou,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Linda Campbell,

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Michael Reed

    Affiliation: Public Library of Science, Development Team San Francisco, California, United States of America

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  • Published: August 18, 2014
  • DOI: 10.1371/journal.pone.0000000

Abstract

Background

On the eve of PLOS' tenth anniversary, we’re pleased to announce that the redesign of all PLOS journals is now live. The goals of the project were to:

  1. Improve reader ability to quickly assess the relevance and importance of an article through a figure browser and highly visible article-level metricsd.
  2. Improve navigation within the site and discoverability of content.
  3. Launch a flexible and extensible platform from which to build out new innovations moving forward.

This initiative offers users more effective ways to access and read content, updates the overall appearance of the sites and harmonizes them with our new PLOS look announced in 2012.

Introduction

Many of you will have noticed some ongoing enhancements to the journals this year, for example figures and Article-Level Metrics (ALM). You can expect similar developments to continue to roll out starting in early 2013 and into the future as we continue to adapt to meet user needs .

After extensive research into how researchers find and use content, we’ve focused our attention on refining and improving our article layout and functionality so that we can help you to locate relevant articles more quickly and enrich your reading experience. Here’s a brief rundown of the new user features that you can see from today:

  1. More prominent figures – featured throughout articles and search so that you can quickly determine if an article is relevant.
  2. Enhanced Discovery – Search now reflects our new expanded taxonomy of subject categories.
  3. Figures in search results - Sort search results by article figures, browse the article abstract and download the article PDF right from the search results.
  4. Metrics Signposts – sub-sets of ALM data, provide at-a-glance measures of article reach and impact.
  5. Custom Saved Search – log in, enter your keywords and save, then receive new content that precisely meets your interests via email.
  6. Author data – clear presentation of affiliations/attribution for each author as well as grouped by institution.
  7. Abstract and Figure viewer – providing new ways for you to get around and find what matters.
  8. Faster navigation – persistent (so you never get lost) and floating (follows you down the page).
  9. Clearer Tabs – easier to see and use, providing enriched article information.

New Technologies

PLOS is taking advantage of the most powerful web technologies to improve our reader experience, promote Open Access and encourage conversation around the latest research to accelerate progress in science and medicine and lead a transformation in research communication.

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Figure 1. The PLOS development team on August 18th, 2014, my have we grown

The PLOS development team on August 18th, 2014 From left to right: Michael Walsh, Jack LaBarba, Matt Bowen, Jeffrey Gray (back), Jonathan "Jono" Finger (front), Holly Allen, Eric Lopatin, Kyle Pang, Fernando Cabrales, John Callaway, Bill Oconnor (back), Polina Grinbaum (front), Jennifer Song, John Bertrand (back), Sahar Aghajani (front), Ryan Skonnord (not pictured: Matt Willman and Mamta Singh)

doi:10.1371/journal.pone.0000000.g001
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Figure 2. PLOS Development Team circa December 18, 2012

The PLOS development team at the release of Ginsu on December 18, 2012. From left to right: Srujana Tumu, John Callaway, Joe Osowski, Eddie Dickey, Jennifer Song, Juan Peralta, Bill O'Connor, Sarah Burt, Jackie Yao, Mike Baehr, Mamta Singh, Ryan Skonnord (not pictured: Richard Cave and Rajani Samidi) #gizu_temp

doi:10.1371/journal.pone.0000000.g002
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Figure 3. PLOS Development Team circa November 11, 2011

The PLOS development team at the release of Ambra 2.0 on November 11, 2011. From left to right: Richard Cave, Alex Kudlick, Scott Sterling, Mike Baehr, Jennifer Song, Eddie Dickey, Bill O'Connor, Joe Osowski, Zoe Mclaughlin

doi:10.1371/journal.pone.0000000.g003

PLOS is proud to have self-funded this project using revenue generated from its publishing business. It’s of prime importance for us as a non-profit that we give back to the researchers who publish with us and what better way to say thank you than with an improved journal experience.

Here’s what Kristen Ratan, PLOS’ Chief Products and Publications Officer, had to say about this project. "PLOS' top priority is meeting the needs of our researcher community and the new sites focus on accessing and assessing the article content and data as quickly as possible. The enhanced publishing platform will also allow us to quickly deploy new functionality and take our reader experience to a whole new level. We look forward to continuing to roll out improvements over the coming year and enriching our content still further".

Contributing to the Assessment of an Article

The PLOS Web site employs a system for the assessment of articles that combines pre- and post-publication peer review [1].

Commenting on an Article

Comments can be used to highlight a minor point, #ginzu_temp, to make additions or clarifications, or to identify and link to material, including more extensive discussions, presented elsewhere. Anyone, including authors, can reply to a comment so that a conversation can develop around an article. Comments can be extended by replying to any comment in the discussion thread. This allows for multiple branching threads of discussion.

All registered users are able to add a Comment to any article. Anyone can register as a user. Users are required to unambiguously identify themselves and to supply a valid e-mail address in order to register. Registration information will be kept strictly confidential by PLOS staff unless otherwise indicated. PLOS reserves the right to suspend the privileges of any registered user. Comments are not anonymous. Please view the PLOS Privacy Statement [2] and the Terms of Use [3]summary for more information.

How to Add and View Comments

To add a general Comment about the article, first make sure you are logged into the Web site. To create a Comment, click the "Comments" tab above the article. Enter a title and text for your Comment in the appropriate boxes.

We advise that Comments are first written in a word-processing program that allows for spell checking before they are copied and pasted into the Comment field. When you are satisfied with the text, click "Post" to attach the Comment to the article. Any correctly formed URLs in the Comment text field will automatically become working links.

How to Add and View Corrections

Authors and other users can post two kinds of Corrections: Minor Corrections and Formal Corrections. Minor Corrections indicate small errors and clarifications to the article, whereas Formal Corrections are reserved for errors that significantly affect the utility or understanding of the article. Formal Corrections are also sent to PubMed Central and PubMed. In both cases, the decision to indicate a posting as a Minor or Formal Correction is the responsibility of PLOS staff.

To make a Correction, first make sure you are logged into the Web site. Click on the "Comments" tab above the article. Enter a title and text for your Comment in the appropriate boxes. When you are satisfied with the text, click "Post" to add the Comment to the article.

To request that a Comment be changed to a Correction, click the "report a concern" button in the bottom-right of the Comment. Indicate why the Comment should be reviewed ("Other"), enter additional information in the text box, and click "Submit". After the Comment is reviewed, it will either stay as a Comment or be changed to a Minor Correction or Formal Correction.

Once a Comment is changed to a Correction, the Correction is displayed on the article. Minor Corrections are listed below the article text. Formal Corrections are displayed above the artcle text.

Responding to Comments and Corrections

To respond to a Comment, click the "respond to this posting" button in the bottom-right corner of the Comment. Enter a title and text for your response in the appropriate boxes. We advise that responses first are written in a word-processing program that allows for spell checking before they are copied and pasted into the Comment field. When you are satisfied with the text, click "Post" to attach the response to the Comment . Any correctly formed URLs in the response text field will automatically become working links.

Following this procedure, an unlimited number of branching threads can be anchored to an initial Comment. If any contribution is removed following moderation, all subsequent responses along its thread will also be removed.

Good Practice

All contributions must conform to the norms of civilized scientific discussion. Any contributions that do not meet these standards will be removed. Any users who consistently transgress these conventions will have their user privileges removed.

A partial list of discussion standards includes the following:

  1. Language that is insulting, inflammatory, or obscene will not be tolerated.
  2. Unsupported assertions or statements should be avoided. Comments must be evidence-based, not authority-based.
  3. When previously published studies are cited, they must be accurately referenced and, where possible, a DOI and link to a publicly accessible version supplied.
  4. Unpublished data should be provided with sufficient methodological detail for those data to be assessed. Alternatively, a permanent Web link to such information should be provided.
  5. Arguments based on belief are to be avoided. For example the assertion, "I don't believe the results in Figure 2." must be supported.
  6. Discussions should be confined to the demonstrable content of articles and should avoid speculation about the motivations or prejudices of authors.

Requesting Review of Inappropriate Content

To request review of a Comment you believe to be inappropriate, click the "report a concern" button in the bottom-right of the Comment. Indicate why the Comment should be reviewed ("Spam," "Offensive," "Inappropriate," or "Other"), enter additional information in the text box, and click "Submit". PLOS staff will investigate the concern, which may involve consulting external experts if necessary. Any Comments that PLOS staff deem to be inappropriate will be removed. Any users who consistently posts inappropriate material will have their user privileges removed.

PLOS is the final arbiter of the suitability of content for inclusion in the PLOS Web sites.

Comment F.A.Q.

Question 1: I have just read a peer-reviewed article in one of the PLOS journals. What do I do next?

Comment on the article - tell us what you think of it. This will help build on the article's research and start a discussion with your peers.

Question 2: But I am not an expert in the field!

That is perfectly OK - nobody can be an expert on everything. But you have read this article because you were interested in the topic and understood some, most, or all of the article. Thus, you are an educated, informed reader. A Comment or question that you post will be worthwhile and of interest to others.

The authors, referees and academic editors of PLOS articles are encouraged to respond to your c omments and questions. They have put a lot of hard work into the manuscript and will appreciate compliments as well as polite criticisms and questions from both experts and non-experts.

Comments that are entirely off-topic, or offensive, or posted by purveyors of pseudo/non/anti-science, will be deleted. If you notice an inappropriate Comment, please flag the Comment so that we can evaluate it and act accordingly.

Question 3: Q: I think the article is well done, well written and complete. I have nothing to ask, critique or add to it. I also think that the paper adds another piece to the puzzle, is not controversial and does not challenge existing theory. Good, but not exciting. Should I say anything?

Yes. PLOS welcomes such articles. Post a Comment stating your opinion nonetheless. Congratulate the authors on good work and note that you think it is a valuable addition to the existing body of knowledge without being revolutionary.

Question 4: I think the article is challenging the current dogma in ways that make me excited about the new view. But I may have quibbles with some details.

Post a Comment on the article that shows your excitement about the work, as well as voices your minor concerns.

Question 5: I think the article has a major problem, but I am afraid to challenge a big name in my field.

Your nervousness is understandable. But if you believe that you have identified a real problem with the article and you feel confident , it is likely that other readers will feel the same. Be the first one to Comment about it (try to use non-confrontational language such as 'could' not 'should' etc) and read the responses of others who may agree or disagree with you. On the PLOS journals, everyone is equal and everyone is expected to treat others with equal respect. Courage to challenge authorities will gain you a fair reputation among your peers.

Question 6: What is in it for me? Why should I spend my time and expose myself to do this?

Think of it in a long-term perspective. Post-publication review is likely to spread over time and become ubiquitous. Within a year or so, all PLOS journals will have this functionality. Other publishers are likely to follow suit. People who Comment frequently and write valuable Comments will build reputations over time. If you comment on PLOS papers now, you will be one of the early adopters and will be recognized and respected for this in the future. Also, prolific commenting may result in offers for future scientific collaboration or employment. This has already happened to prolific commenters on science blogs and is even more likely to happen to prolific commenters on peer-reviewed articles.

Secret

Search for a research article with the term "ginzu" in it. Scroll Down, ALT-SHIFT left click on the X in the upper right corner. Find the term "ginzu" in the body of the article. Click on it, enjoy.

More Information

For more information about commenting on papers, including the technical details, see the Comment Guidelines.

Then charge ahead and get started - join the community!

Acknowledgments

We acknowledge the guidance of Drs H. Varmus, P. Brown, M. Eisen, and J. Omura. Special thanks to past contributors from the Topaz development team (Stephen Cheng, Eric Brown, Joycelyn Chung, Amit Kapoor, Pradeep Krishnan, Ronald Tschalär, Ed Yoon) and from PLOS[4] (Susanne DeRisi, Dragisa Krsmanovic, Alex Kudlick, Zoe Mclaughlin, Mark Patterson, Nick Peterson, Margaret Shear, Scott Sterling, Russell Uman, Bora Zivkovic).

Author Contributions

Conceived and designed the experiments: RC. Analyzed the data: The Scientific Community. Wrote the paper: RC.

References

  1. 1. Public Library of Science (2008) PLOS Guildelines for Commenting, http://www.plosone.org/static/commentGui​delines.action.
  2. 2. Public Library of Science (2008) PLOS Privacy Statement, http://www.plosone.org/static/privacy.ac​tion.
  3. 3. Public Library of Science (2008) PLOS Terms of Use, http://www.plosone.org/static/terms.acti​on.
  4. 4. Public Library of Science (2012) PLOS Staff, http://www.plos.org/about/people/staff/.