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The Canadian Open Neuroscience Platform: Catching Up to Plan S and Going Further

Guest Authors: Dylan Roskams-Edris (Open Science Consultant and Invited Scholar with the Center for Genomics and Policy,), JB Poline (Associate Professor, Neurology and Neurosurgery, McGill University), and Nikola Stikov (Associate Professor, Department of Electrical Engineering, Polytechnique Montreal).

First off, what is Plan S and why does it matter?

In September 2018 a group of European funding agencies, along with some private funders, assessed how scientific information is disseminated – namely that university researchers receive public funding, perform experiments, collect data, write articles about the results, review each other’s articles, and then the publicly funded institutions they work for foot the ever increasing bill to buy access to all this work – and decided enough was enough; publicly funded science should be publicly accessible.

They formed cOAlition S and announced Plan S which, boiled down, says that after 2020 any work funded in whole or in part by the members of the coalition must be published in journals that allow immediate, free, and public access to articles. They also published a set of guidelines and best practices that journals publishing funded research must follow. Those interested in the details of Plan S are encouraged to read about them here.

Only 5 months after Plan S was revealed, the University of California system – one of the largest and most well-respected public academic systems in the world – announced that they were ending their relationship with the publisher Elsevier. The split was due primarily to Elsevier’s refusal to make all UC published research open access on the UC’s terms.

These efforts are a great start.

For those actively working to open global research efforts, however, efforts like Plan S are only the beginning. The push for open science is much larger than making scholarly articles open access. Open science demands that the data, software, materials, and know-how that enables science are also shared – or better yet, openly published.

Sharing, Publishing, and Open Access Articles

It is worth pausing here for a brief aside about the distinction between open sharing, open publishing of research resources, and open access publishing of articles. All of these are important but for open science to be successful the distinction between them has to be clear.

Open sharing consists of making research resources available in a way they can be freely accessed and used. Sharing datasets in a repository or data sharing platform like Dryad, or code used for data analysis and visualization via a service like Github, are good examples. Sharing in this way rapidly disseminates resources and makes them available for use and adaptation by others as quickly as possible. Open publishing of research resources, however, involves the filtration of these resources through other researchers. These peer researchers make sure that the shared resource – whether it is data, code, single figures, or any of the plethora of resources developed throughout the scientific process – is in a form that is standard and easily usable by others, as well as presenting those resources in a curated form on a website or repository. Open access publishing of articles is the primary target of efforts like Plan S and relates to publishing scholarly articles in such a way that they are freely accessible and usable.

The Canadian Open Neuroscience Platform (CONP), along with myriad other organizations, are developing the resources needed to enable open sharing, open publishing of research resources, and open publishing of articles. By doing so the CONP is helping open science and reduce the current inequalities in access to all of the tools and research outputs science needs to thrive.

Beyond Publications

Assessing the situation here in Canada, the current open access policies of Canada’s primary trio of scientific funding agencies take a weaker stance than Plan S and, as we’ve already argued, efforts like Plan S are only a start. Even if Canada were to suddenly marshal its forces of scientific-policy and follow the lead of cOAlition S we would still be well behind where open science should be. Scholarly papers are just the tip of the iceberg of scientific discovery. Any given publication is the result of months of work involving data collection, coming up with hypotheses, planning experiments, carefully recording progress in notebooks, developing software, analyzing results, writing drafts, and working with editors. The iceberg metaphor is a good one; the publication, like the burg’s tip, is what is seen, but floats atop a much larger body of work that supports it.

Open science in its full and rich instantiation is about sharing and publishing all as many scientific resources as possible to enable collaboration throughout the research process. It grows from the simple idea that working together is more effective than working in silos; that many hands make light work and many eyes spot more errors. In order to work together scientists need to be able to freely discover each other’s work and use each other’s resources, not just have access to the polished end result. Doing so will improve replication, catch errors in methodology early on, and prevent redundancy, all while reducing unnecessary barriers to discovery and outlays from the public coffers.

The internet and modern computing technology make this dissemination possible. What we need now is for funders, institutions, and scientists themselves to commit to encouraging and enabling the sharing their data, code, notebooks, experimental protocols, draft manuscripts, and all the other pivotal elements of discovery.

Building on Plan S

Plan S does mention the sharing of scientific data. On their Principles and Implementation page they encourage the sharing of research resources underlying publications in repositories that make the resource “as open as possible and as closed as necessary”, as well as highlighting resource sharing as a key topic of negotiations between journals, funders, and institutions. Doing so, however, requires repositories where data and code that can be stored, data sharing platforms where that data can easily linked to publications, as well as organized curation efforts to make sure the linked research resources are usable by others.

The CONP is building exactly these resources for the neuroscience community. It is collaboratively developing the user portal, online publishing, informational resources, and governance and policy mechanisms that will enable neuroscientists to disseminate each component of their work as openly as possible, and to keep them open. The CONP scientists and stakeholders believe that these resources will catalyze collaboration and accelerate neuroscientific discovery.

What’s Needed Now to Go Further

But more is needed.

Opening science requires the collective effort of funders, data sharing platforms, academic institutions, and individual scientists. Science doesn’t have to be opened all at once, but steps down the open road must be taken, and must be taken now. The CONP will provide tools and guidance, but scientific culture shift requires a concerted community effort.

Some first steps needed to enable the open publishing of all research resources include: (1) forging agreements and partnerships between journals and open science platforms to make it easy for scientists to share their data, publish it in a curated form, and link it to publications, (2) promotion and tenure policies at academic institutions that value the sharing and publishing of data on par with producing articles, (3) funding agencies that require (and enforce) sharing and publishing data, code, and materials associated with publications as a condition of receiving a grant, and (4) a commitment from scientists themselves to change the culture of science towards openly sharing and publishing as many of their resources as they can.

Get to know an Academic Editor: Karen Root

Note: PLOS will be attending the ESA conference in Louisville, Kentucky starting on August 11. Stop by our booth and say hello! Dr. Karen Root, an Academic Editor for PLOS ONE, will also be in attendance. You can meet her at our booth on Monday, August 12 between 3 and 4pm. Here’s a brief interview with her. 

Q: What is your area of study and what are you currently working on?
A: I originally began as behavioral ecologist but realized there were real issues in the population that I was studying related to human activities. Conservation biology drew me since it provided a way to utilize my ecological training to directly address some of those issues. My current research focuses on native species and the factors that imperil them, but also on the effects of restoration and management.

Q: What first drew you into the field?
A: I have always been interested in the natural world around me, especially growing up in an urban center. During college I spent a summer at the Itasca Biological Station and fell in love with field work. In graduate school, I grew to appreciate techniques such as spatial analysis and population modeling that complemented the field studies. Conservation biology is a way to integrate all of these approaches.

Q: Could you share your thoughts on why this type of research is important? How does it affect other areas of research? Other communities?
A: I think of myself as a practical ecologist–basic ecological research is important but there are issues that need to be addressed. When I can demonstrate the societal value of my research, I receive more support, collaboration is more likely, and scientists and non-scientists alike are more receptive.

Q: How long have you been an editor on PLOS ONE? What have you enjoyed most about it?
A: I have only been an editor for a year, but it has been a very interesting experience and I have learned so much more about science communication.

Q: Why is PLOS ONE important to you and the ecology community?
A: I appreciate the inclusivity of PLOS ONE. It is very tempting to focus on one aspect of ecology or a particular subdiscipline but you would miss out on all of the other interesting research out there that can strengthen your own science.

Q: What advice would you give to authors in your field who are getting ready to submit their work?
A: Read broadly. If I can understand a paper that is not in my area of expertise, then I can learn something important about how to write more effectively.

Q: What are you most looking forward to while attending ESA?
A: One of my favorite aspects of ESA is the chance to catch up on the latest advances not only in ecological science but also education.

Q: Are there any trends in your field right now that you’re hoping to learn more about?
A: There are so many new ways to communicate about science and become more effective.

Q: Why do you believe in Open Science?
A: Problem solving requires cooperation, coordination and large amounts of data to be truly effective. Open Science can facilitate these aspects as well as increase the diversity of participants and disciplines in the process.

PLOS Computational Biology announce reproducibility pilot

At PLOS Computational Biology, one of our driving motivations is to provide services and support to our community of authors, editors, reviewers and readers. Transparency and reproducibility in peer review and reporting of results are two key aspects of that mission, and we are very pleased to announce a pilot on the journal that aims to support both of these aspects of publishing.

Our Managing Editor, Gary Beardmore, and Editor in Chief, Jason Papin, have been working with the Center for Reproducible Biomedical Modelling. Through this collaboration we will soon be able to offer expert technical peer review specifically checking that submitted systems biology or physiology-based models run according to the results presented in the manuscript submitted to the journal. The peer review will be delivered in addition to our usual scientific assessment of the manuscript, and for the duration of the pilot it will be optional for authors to take part. The expert peer reviewers will be eligible for inclusion in our collaboration with ORCID to get credit for the review work that they complete. Furthermore, as for all manuscripts published at PLOS Computational Biology, authors will have the option to make the expert review open – alongside the other reports on the manuscript – in our published peer review.

We plan to monitor the pilot and to report back on the results next year. The aim is for the review process to be completed in the usual time frame for manuscripts at the journal, and for authors to feel that it provided them with additional guidance regarding the reporting of their models. Overall, we hope that this pilot will contribute to making it easier for interested readers to reproduce and build on models published in the journal – supporting the science going forward.

Original image by Rita Bhui

https://journals.plos.org/ploscompbiol/article?id=10.1371/image.pcbi.v13.i05

 

 

 

Get to know an Academic Editor: Lars Juhl Jensen

Note: PLOS will be attending the ISMB/ECCB conference in Basel, Switzerland starting July 21. Stop by booth 7 and say hello. Lars Juhl Jensen, an Academic Editor for PLOS Computational Biology, will also be in attendance. Here’s a brief interview with him. 

Q: Can you tell us a little about yourself?

A: I was trained as a chemist but grew up programming, so bioinformatics was an obvious match for me. I started in the group of Søren Brunak, where I did my training including Ph.D. and then spent six years at EMBL in the group of Peer Bork before starting my own group at the Novo Nordisk Foundation Center for Protein Research in 2009.

Q: How many years have you been an editor on PLOS CB?

A: I’ve been associate editor on PLOS CB for 11 years.

Q: Why is PLOS CB important to you and the community

A: PLOS CB plays an important role in bridging the gap between the more algorithm-focused bioinformatics journals and the traditional biological journals, which rarely publish studies that do not have a wet-lab component.

Q: What is your area of study and why is it important?

A: My group has a strong focus on tool development, primarily related to biological networks and biomedical text mining. Network representations of the current biological knowledge and available data, including what is buried in the literature, is increasingly important for interpreting new omics data.

Q: What first drew you into the field?

A: With an interest in molecular biology and many years of programming experience, it was really a no-brainer to go into bioinformatics back when the first fully sequenced genomes became available.

Q: What are you most looking forward to while attending ISMB?

A: The most interesting sessions to me are the NetBio COSI and special session on text mining, which I am involved in organizing. Besides that, the poster sessions are always a highlight for me.

Q: Are there any trends in your field right now?

A: Deep learning is obviously a major trend in text mining. Other than that, the move towards open licenses on databases and tools continues to be strong.

Q: Why do you believe in Open Science?

A: In my experience sharing the tools we make already before publishing them is highly advantageous. If you already have a user base before submitting a manuscript, it only becomes easier to publish your work. Editors can see that it is worthwhile publishing, most bugs will have been sorted out before peer review, and the publication is more likely to get cited as soon as it comes out.

Birds, bees, Beethoven–and other PLOS research making June headlines!

New research from PLOS ONE shows that flowers near managed hives may be one of the sources of virus transmission from infected honey bees to wild bumblebees. 

Lead author Samantha Alger summarizes:  “The study supports a widely accepted yet largely untested hypothesis: viruses are spilling over from managed honey bees into wild bumble bee species and this is likely occurring through the shared use of flowers,” noting that careful monitoring and treatment of diseased honeybee colonies could help mitigate the damage from these viruses to wild bees. Read more about this work on the Economist, the Independent, and IFLScience.

A recent study from PLOS Biology uses a new device that noninvasively measures blood flow and oxygenation in the brain and blubber of harbor seals to better understand the biology behind mammalian diving. The device showed that harbor seals routinely reduced blood flow to their blubber, thereby slowing oxygen consumption, around 15 seconds before diving into water. This indicates the seals have conscious control over their dive reflex (previously thought to be a purely automatic response). 

Dive deeper into these findings at the New Scientist and the Daily Mail. 

Another recent paper from PLOS Biology describes how birds of a feather flock together–even when it’s more energetically costly to fly as a group. The authors compared the flight characteristics of solo and paired pigeons making a 7km flight, and found that paired individuals had improved homing accuracy (which reduced the flight distance and time); the cost of this accuracy was an increase in speed and wingbeat frequency compared to solo fliers. The fact that pigeons are willing to pay this energetic premium underscores the importance of flocking together.

Lead author Lucy Taylor adds: “The results of this study were completely unexpected. Energy is the currency of life so it’s astonishing that the birds are prepared to pay a substantial energetic cost to fly together.”

 Read more at the New York Daily News and New Atlas, or check out a video at DailyMotion.com

Finally, a new study from PLOS ONE mathematically characterizes Beethoven’s string quartets for the first time, applying statistical and data science techniques to reveal recurring patterns in the great composer’s music. 

Read more at Forbes, Cosmos Magazine, and The Week–and have a listen to the string quartets inspiring this work, too.  

 

You’ve completed your review – now get credit with ORCID

 

For more than five years, PLOS authors have used ORCID to make their professional lives easier. Now reviewers at PLOS can take advantage of the same benefits to track their contributions, claim credit, and build up their research profiles.

Same ORCID, now for reviews

Starting today, reviewers can enter their ORCID iD in the Editorial Manager submission system for all PLOS journals and opt-in to automatically get credit when they complete a review, the same way they would for their published articles. The ORCID reviewer record does not contain details about the specific manuscript and we’ve introduced a delay, so reviewers can track their work even while retaining their anonymity.

Being able to record more types of work is especially important for researchers who are working to build up their scholarly reputation. For those who are getting ready to apply for funding or a new position, credit for reviews helps demonstrate the full breadth of their contributions to the field.

“We thank PLOS for partnering with ORCID to provide their reviewers the opportunity to get credit for their critical contribution to the research ecosystem.”

– Laure Haak, Executive Director of ORCID.

 

More ways to get credit = more reasons to review

Reviewers’ contributions to the publication process are essential. They are working researchers who give their time and expertise to help authors improve their work and help editors decide when a manuscript is ready to become part of the permanent scientific record. But recognition for reviews often flies under the radar, in part, because tools for tracking these contributions without compromising anonymity may not be available.

Earlier this year we rolled out options for signed and published peer review history. Combined with ORCID, we aim to give reviewers the tools and opportunities to claim credit for their reviews in a way that works for them.

 

Write great reviews           Get credit          

Peer reviewer center

Signed peer review

Peer review toolbox

Peer review history

 

How it works

ORCID is a persistent unique identifier that distinguishes you from other researchers with the same name and sticks with you throughout your careers. Even if you change your name, switch institutions, or move to another country, all of the contributions tracked by your ORCID are still identifiable and attributable to you

If you don’t already have an ORCID iD, you can sign up on the ORCID website. Then, follow the instructions on our site to link your iD to your Editorial Manager profile.

Once your ORCID is linked, you can opt-in to automatically alert ORCID anytime you complete a review. For each new review, you’ll get a message with the option to post the citation to your ORCID record. Click “authorize” to start tracking your contributions.

 

Published Peer Review (community comments)

In February, we asked researchers about the biggest change they hope to see in Open Science. Nearly 3,000 of you weighed in. Here’s what you had to say…

In May, we introduced published peer review history at PLOS, a modular approach to transparent peer review that invites to you choose the model that works best for you and your particular manuscript. Reviewers decide whether to sign their comments at submission. Accepted authors decide whether to publish peer review history alongside their manuscript. The whole community benefits from a deeper more nuanced view of the peer review process.

What is the community saying about peer review history

“[with] transparency in peer review … the process becomes more fair and clear and, above all, the result of scientific production is more collaborative and effective.”

– Leonardo A. Peyré-Tartaruga, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil

 

“I think signed peer review will help legitimize the peer review process as a scholarly output instead of a service commitment. It will also encourage researchers to participate in a more thoughtful process and can provide a valuable contribution to the study’s scientific record.”

Carrie Dolan, William and Mary, Williamsburg, Virginia, United States of America

“[open peer review] improves auditability of the article itself and the journal’s processes and thoroughness…It also helps build public trust in the process by removing the mystery of secret academic peer review, as well as showing the robustness of the method in action.”

– Thomas Shafee, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia

“Peer review is more essential and relevant today as it has ever been.  We are entering an era where there is limitless information with very limited means to understand it value. As a scientific community, we need to engage the public more often.  A part to this is helping them understand the peer review process and how it leads to the discoveries of tomorrow.”

Scott Pegan, University of Georgia, Athens, Georgia, United States of America

“Transparency in peer review may develop the quality of research and reduce research misconduct. So everyone can see clearly on the how, what, and why behind the editorial decision making. This is about trust, and trust is one of the important things in the scholarly publication.”

– Monika Oktora, University of Groningen, University Medical Center Groningen (UMCG), Groningen, The Netherlands

Spreading the Word: PLOS Advances Research Through Media Partnerships

Last year, PLOS helped more than 2,300 articles receive media coverage in high-profile outlets including The New York Times, the BBC, National Geographic, Scientific American and The Washington Post. How do we do it? For starters, our press team sends out on average one press release per day, garnering the attention of the 1200 journalists on our press list, plus members of the media who haven’t heard of us yet.

But for us to make sure your research gets the recognition it deserves from other researchers, potential funders, and policy makers, our dedicated media team also leverages a robust network of partnerships to connect science and the media.

Science for non-scientists

Though all PLOS research is Open and accessible to everyone, many readers depend on journalists to distill complex scientific concepts for broader consumption. An important link in the transformation of Research Article to NY Times cover story are Science Media Centers (SMCs) which work with journalists to get the public access to the best scientific evidence and expertise.

Through SMCs, journalists can find “sources” or vetted experts in a given field to help add context to the research they’re reporting on. Some SMCs, such as SciLine, also offer fact sheets summarizing popular topics that have been reviewed and verified by experts.

We have been working with SMCs in the UK, US, Canada, Australia, New Zealand and Germany for over a year, for example by providing information that helps SMCs spread the word about PLOS work even further. In Europe, we also collaborate with the European Science Media Hub, part of the European Parliament, whose work helps facilitate the transfer of knowledge and training between the European Parliament, the scientific community, and the media.

Our partnership with these organizations is also helping us to shape best practice for communicating research, especially for new scholarly outputs like preprints.

Leveraging your network and your expertise

Perhaps the best place to seek promotion and recognition for your work is your own institution. Already, we work with top-tier institutions such as MIT, Harvard University, University of Cambridge, University of Oxford, the National Institutes of Health and more to help them promote the amazing research being done by their affiliated PLOS authors. We’re hoping to expand this program further, but even without formal partnership, we encourage all authors to contact their institution’s press office when their research is accepted for publication – your colleagues’ networks can be a huge asset to your career.

For authors who are keen to be hands-on in disseminating research, we also recommend contacting our partner Science Trends. This free platform allows authors to write their own “self-directed press release” in under 500 words which is then published on Science Trends and on social media to an audience of 500,000 followers. You can find more information on our website.

We’re dedicated to providing the best experience for our authors, pre and post-publication. We’ll continue innovating and promoting your work and we want you to feel empowered to do so as well. Check out our media toolkit for tips on publicizing your work, speaking to the media, and stepping up your social media game. Of course, our media relations team, Beth Baker and Charlotte Bhaskar, are always happy to help – contact them at onepress@plos.org.

 

The origins of avian flight, thermostat battles heating up, and other PLOS research making headlines in May!

New research from PLOS Computational Biology uses robots, reconstructed model dinosaur feathered forelimbs, and juvenile ostriches to simulate the first potential avian flight stroke in dinosaurs. This study shows that running on the ground naturally stimulates a flapping motion in feathered forelimbs, and suggests that this flap may be the origin of avian flight.

Author Zhao explains: “Our work shows that the motion of flapping feathered wings was developed passively and naturally as the dinosaur ran on the ground…although this flapping motion could not lift the dinosaur into the air at that time, the motion of flapping wings may have developed earlier than gliding.”

See videos of the robots and young ostriches strutting their stuff, and read more on CNN and Gizmodo.

http://blogs.plos.org/plos/files/2019/06/journal.pcbi_.1006846.s008.mp4

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A new study from PLOS ONE found that that in a test room set to temperatures ranging from 16.19 C/61.14 F -32.57 C/90.63 F, female study participants performed best on math and verbal tests at the higher end of the temperature range, while male participants performed most strongly on the same tests at lower temperatures. This is the first experimental research supporting anecdotal and survey responses indicating women tend to prefer warmer room temperatures than men, by showing that temperatures can affect both comfort and performance.

Authors Kajackaite and Chang summarize: “In a large laboratory experiment, over 500 individuals performed a set of cognitive tasks at randomly manipulated indoor temperatures. Consistent with their preferences for temperature, for both math and verbal tasks, women perform better at higher temperatures while men perform better at lower temperatures.”

Check out more of this hot topic as featured on the Guardian, the New York Times, Fox 5 News (with a video featuring author Tom Chang), and the Atlantic.

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Along a similar vein(!), new research from PLOS Medicine shows that the medical care received by heart failure patients in the UK may have important gaps around diagnoses, insufficient follow-up after hospitalisation, and improperly-prescribed dosages, among other issues; these problems significantly affected women and older people.  

Read more on the Daily Mail and the Telegraph.

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A 2016 mass die-off of puffins and other seabirds in the Bering Sea is reported in a new PLOS ONE study by Timothy Jones of the citizen science program COASST at University of Washington, Lauren Divine from the Aleut Community of St Paul Island Ecosystem Conservation Office, and colleagues. Up to 8,500 puffins and auklets may have died in this event, which appeared to be due to starvation; the authors suggest that climate shifts may have resulted in a lack of prey. Read more about this story on Vice, Discover Magazine, and Scientific American.

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Finally, in lighter news, a new study from PLOS ONE showed that wolves behave more prosocially towards their fellow pack mates than do pack dogs during a touchscreen-based task that allowed individual animals to provide food to others–though the study did not look at the behavior of pet dogs.

Author Rachel Dale notes: “This study shows that domestication did not necessarily make dogs more prosocial. Rather, it seems that tolerance and generosity towards group members help to produce high levels of cooperation, as seen in wolves.”

Check out further coverage on PBS News and Motherboard by Vice.

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Image captions and credits

  1. Seven-rigid-body system of Caudipteryx. The simplified rigid body system illustrates the mechanism of moving parts, main body, wings, legs, neck and head, and the tail of the Caudipteryx. The masses of all parts are represented by lumped mass points and the muscles at the joints are replaced with springs (As damping coefficient does not significantly affect the natural frequency, we simplified the joints which are composed of tendons, muscles, ligaments and soft tissues as purely elastic springs with no damping). Different effective masses of these seven primary modes of the simplified Caudipteryx show different possibilities to be excited. (Talori et al, 2019,  PLOS Computational Biology)
  2. Video: Observation on the juvenile ostrich. The forced vibrations of the wings of the young ostriches are easily found when they run on the ground. (Talori et al, 2019,  PLOS Computational Biology)
  3. Carcasses of tufted puffins, October 2016. (Aleut Community of St Paul Island Ecosystem Conservation Office)
  4. Touchscreen test (Dale et al., 2019, PLOS ONE)

 

Looking Good: Tips for creating your PLOS figures graphics

Enhance your research with tips and tools from the experts on the PLOS Production Team. This post is part of our new Format for Success series where we’ll share advice for generating figures and graphics that make submitting a breeze. Stay tuned for more. 

We know that preparing graphics files can be one of the most challenging parts of submitting your hard work to a publisher, when you would rather be observing in the field, experimenting in the lab, or conversing with the community. Like you, we want your research to shine and be noticed by your peers, adding to the scientific discourse and fostering collaboration in and across disciplines.

To help you create the best images possible and ensure a smooth article production experience, we’ve put together our top tips, distilled to a few major areas, for assessing your graphics files during submission:

  • Consider raster images vs vector imagesRaster images are made of pixels. A pixel is a single point or the smallest single element in a display device. Vector images are mathematical calculations from one point to another that form lines and shapes, which adjust to fit a monitor display and zoom.

Our journal article pages use raster graphics for in-article figure display, the lightbox figure viewer, and carousel thumbnails.  Raster graphics are easier to create, store, and transfer across platforms, but limit resolution to 600 dpi. Alternatively, vector graphics are only available in the article PDF accessed online, but will result in a more detailed image at high zoom.

  • Choose a resolution between 300 and 600 dpi – Effective resolutions below 300 dpi (dots/pixels per inch) often result in a blurry, jagged or pixelated image that is not optimal to publish, and resolutions above 600 dpi frequently must be resized or rescaled. We are required by the PLOS publishing platform, and community indexes like PubMed Central, to ensure content adheres to these resolutions.
  • Combine multi-panel images – Often, it’s useful to exhibit a Part A, Part B, and Part C, all within one figure image. To create a multi-paneled figure from individual images, we suggest using a presentation program like PowerPoint, Word or GIMP to arrange your panels, create labels, and scale or size your figures. Multi-paneled figures need to fit into a single page or be broken apart into separate figures in order to publish clearly and accurately.
  • Flatten image layers – Unflattened images can incorporate alpha channels, which include a transparent layer potentially containing “junk”, “artifacts”. Sometimes, an unflattened image can also render a figure into a complete black or white rectangle, obscuring all your content. We recommend that you flatten your graphics to combine all the layers into a single background layer, so we can ensure the quality of the output equals your intent.
  • Compress file size with LZW compression – Data compression helps to reduce file size and also decreases time required to download and upload content. With compressed files, we can help you reduce the size of your article PDF, improving a researcher’s ability to access your work and send it to colleagues.

Using PACE

To help you assess your figure images, PLOS also offers authors a free, web-based imaging review tool, PACE, that evaluates figures against our platform requirements and fixes the most-common image issues, detailing any changes made, or informs the user what outstanding issues may exist.  PACE compiles two, online review options in the form of typeset page mockups to give users an idea of how the uploaded image would appear in the final article. To use PACE, simply register with your email address: https://pacev2.apexcovantage.com.

Similar to undertaking a scientific protocol, PLOS’s production team follows specific rules to ensure that the accepted content is correctly transformed to XML and PDF in order to publish accurately in our journal sites and syndication targets. In short, graphic images must generally conform to the following:

  • File format – TIFF or EPS
  • Dimensions – Width: 789 – 2250 pixels (at 300 dpi). Height maximum: 2625 pixels (at 300 dpi).
  • Resolution – 300 – 600 dpi
  • File size – 10MB or under
  • Figure files naming – Fig1.tif, Fig2.eps, and so on. Match file name to caption label and citation.
  • Caption – Place within the manuscript as simple text, not within the figure file

We’ve posted additional graphics recommendations, as well as instructions for exporting graphics from specialized software, here: https://journals.plos.org/plosone/s/figures.

We hope these suggestions make figure preparation even easier so you can spend more time advancing your field and we can publish your work faster than ever.  We encourage you to email us at figures@plos.org with further questions.

PLOS welcomes the revised Plan S guidelines

As a fully Open Access publisher entirely ready to support cOAlition S-funded authors, we have always been in a position to give our support to this bold initiative, and entirely agree that the driving principles and overall objective of Plan S have not been lessened or changed. cOAlition S has clearly listened to constructive suggestions from the community, and there is now enhanced scope for continued community dialogue, alongside the forward momentum. There are a number of revisions which we recognize will make the transition easier for the community, and which clarify or acknowledge other important factors, such as:

  • Diversity of models underpinning OA – The clarification that neither Plan S nor OA insists on the APC/publication fee model is a key refinement. While this has been a dominant model of OA publishing (including ours) in the Global North, it is absolutely necessary for any OA policies, plans, or mandates to be clear that OA is the outcome for research, not a single or specific business model;
  • Commitment to research assessment based on intrinsic merit – PLOS is an active member of DORA and appreciates the emphasis on changing the reward and incentive system of research. The OA movement has always operated closely with movements to improve the culture of research, and so we welcome this acknowledgement;
  • Preprints and peer review – PLOS advocates the posting of preprints to accelerate sharing of knowledge and welcomes cOalition S’s  “strong encouragement” for the early sharing of research through preprints while acknowledging that preprint posting alone is not a route to Plan S compliance. The value of high quality peer review as a “significant addition of value to scholarly communication” as emphasized in the Plan S Rationale is recognized at PLOS and was a driver in our move to offer published peer review, giving authors and reviewers more choices about how they publish and claim credit for their work.

The timeline shift for Plan S implementation to 2021 will be helpful to gain even more community support for the initiative. But we (along with many other publishers) remind the community that PLOS is already 100% Plan S compliant, and our suite of seven journals is available immediately for your cOAlition S-funded work  in most scholarly disciplines relevant to Plan S.

PLOS was founded on the principle that scholarly knowledge is a public good. We welcome the bold move of funders aligned behind the fundamental principle that no scholarly publication should be locked behind a paywall.

Depositing and reporting of reagents: Accelerating open and reproducible science.

The following blog was written by Angela Abitua (ORCiD ID: 0000-0002-8059-4050) and Joanne Kamens (ORCiD ID: 0000-0002-7000-1477) from Addgene. PLOS is excited to support reagent repositories such as Addgene as yet another step to improve scientific reproducibility. Open access to research findings and the underlying methods, materials and data, and issues surrounding reproducibility, replication, and research waste will be discussed this June 2-5 at the 6th World Conference on Research Integrity in Hong Kong, where PLOS ONE’s Senior Editor, Renee Hoch, will present a talk on data availability and image integrity.

Without materials and data, there is no research. Barriers to scientific progress can result from something as basic as not having access to reliable, validated information for research materials. That barrier is raised further when scientists cannot obtain samples or data in a timely fashion. Data and material repositories are breaking down these barriers. As a publisher, PLOS is supporting better, more open science by recommending repositories and encouraging use of standardized, unique identifiers for materials.

Centralized depositing of materials advances science in so many ways. It saves authors the time and burden of shipping requested materials. Researchers who request from repositories save time by not having to recreate reagents or wait months or years to receive samples. Many scientists have been on the receiving end of a request that was filled by an incorrect or degraded sample, which further delays research. Repositories like the ones recommended by PLOS handle the logistics of material requests, letting the scientists focus on what’s important: doing research.

For example, repositories make it possible for researchers to get access to different cell lines (American Type Culture Collection, Coriell Institute), plant materials (Arabidopsis Biological Resource Center), organisms (Bloomington Drosophila Stock Center, Caenorhabditis Genetics Center, European Xenopus Resource Centre, Jackson Laboratory), plasmids (Addgene, DNASU, PlasmID) and many other biological materials. Moreover, many of these repositories provide web-based databases that are easy to search and provide openly available information about each material.

For reagent reporting, many repositories also support unique and persistent identification of reagents. Identifiers like Research Resource Identifiers (RRIDs) make it easy for authors to cite materials and improves reporting through standardized identification and a permanent link to information about each reagent. For example, each Drosophila strain at the Bloomington Fly stock Center is assigned a fly stock RRID. For mice, the Mutant Mouse Resource and Research Centers (MMRRC) provides a mouse RRID for mutant mouse strains. For plasmids, Addgene will automatically register a plasmid RRID upon deposit.

Depositing increases materials transparency and reproducibility

Addgene currently contains over 70,000 unique plasmids and has distributed over 1,000,000 plasmids worldwide since 2004. At Addgene, depositing plasmids is free and straightforward, with the added bonus that it provides quality control measures that contribute to improved reproducibility. Addgene performs full plasmid sequencing and each plasmid is assigned a unique RRID identifier, along with a plasmid webpage that provides sequence data, cloning information, and associated protocols. This ensures researchers have detailed information about each plasmid reagent. Moreover, each Addgene plasmid page provides an Articles Citing this Plasmid section which allows researchers to learn how the plasmid was used and validated by different labs.

Recognition and credit for depositing authors

Depositing materials at the time of publication also provides benefits to both authors and publishers. Depositing authors gain recognition and are cited whenever requestors use the published materials in their own research articles. In fact, data from Addgene supports that depositing published plasmids in Addgene’s repository increases their use and results in increased article citations. Deposition at the point of publication also ensures timely distribution of materials. Finally, the information linked to each deposited reagent serves as reliable open data for the materials reported in the publication, simplifying the manuscript-writing process. Overall, PLOS’s support of reagent repositories, follows the publisher’s steps in improving data availability and protocol sharing and is a welcome addition for improving materials access and scientific reproducibility.

New sharing practices will change science for the better

By encouraging authors to deposit materials at the time of publication, journals will help accelerate research through timely distribution and accurate identification of reagents. Biological repositories exist to serve the scientific community. Take Addgene’s involvement in the explosive advancement of CRISPR research. Since 2012, over 8,400 CRISPR plasmids have been deposited and Addgene has distributed over 144,000 CRISPR plasmids worldwide, enabling researchers to share, modify, and improve this game-changing molecular tool. It is a prime example of the positive impact that biological repositories are making on research.

Thanks to PLOS’s updated recommendations, the importance of depositing and sharing reagents is finally getting some much-needed recognition. If the positive outcomes of PLOS’s data availability and protocol sharing policies is any indication of what’s in store for open material sharing, the future of science looks bright: speedier, more transparent, and more reproducible research.

PLOS Journals Now OPEN for Published Peer Review

 

Starting today, ALL PLOS journals will offer authors the option to publish their peer review history alongside their accepted manuscript! We’ve been excited to make this announcement, and make major strides towards a more open publication process, since last fall when we signed ASAPbio’s open letter committing to transparent peer review options.

What will it look like?

Our philosophy going into this project has been to open up the peer review process in a way that gives authors and reviewers more choices about how they publish and claim credit for their work.

As before, our peer review process defaults to single-blind, although reviewers have the option to sign their names to their reviews if they wish. What we’ve added to our process is an option at acceptance for authors to decide whether to publish the full peer review history alongside their work. This package includes the editor’s full decision letter, complete with reviewer comments and authors’ responses for each revision of the manuscript. Peer review history will have its own DOI enabling reviewers to take credit and earn citations for their contributions. If the reviewers have chosen to sign their reviews, their name will also appear on the published reviews but they can also chose to remain anonymous.

All manuscripts submitted after May 22, 2019 will be eligible for this option if accepted at a PLOS Journal. Here’s a look at the variations of open our opt-in model provides:

 

A major step for PLOS, and scholarly communication

The peer review history reveals crucial perspectives and decisions that supply additional context for readers and researchers. Because of the potential benefits, we’re making this option available now on all seven PLOS journals.

Other journals that have experimented with published peer review models have shown that the quality of feedback provided is at least as good as other models – we think it has the potential to be even better through increased accountability and transparency. We’re building off the foundations and lessons learned by these examples and are confident our model can offer authors more choices to make their research and the publishing process open, and showcase the rigorous review of their work.

Through the scale of our publishing output across all seven PLOS journals, we see this as an opportunity to make a significant change in the scholarly communication landscape and lay the foundation for a more open view of the manuscript handling process from start to finish.

Open beyond Open Access

While the benefits of transparency are numerous, we see published peer review as a crucial first step towards solving two fundamental problems: reviewer credit and public understanding of the peer review process. So far, Open Access has made it possible for research to reach a global community of readers but we have not yet demonstrated the work that goes on behind the scenes to validate scientific claims.

Publishing peer review history is a means of enriching the scientific record by giving context to evaluation and publication decisions. We hope this is also an important step toward elevating peer reviews to scholarly outputs in their own right that reviewers can take credit for.

In conjunction with the work it describes, peer review history can also be a source of material for educating students and the general public about peer review. Our content is also machine readable, paving the way for deeper analysis and discussion by the community.

Looking ahead

We’ve developed this option in consultation with our editors who are dedicated to improving our journals, and we also committed to reporting back our findings. As we learn more about how published peer review shapes author and reviewer choices, and reader experience, we’ll continue to update you on what we find.

 

PLOS Receives Meritorious Achievement Award from the Council of Science Editors

We are honored, and humbled, to receive the 2019 CSE Award for Meritorious Achievement. The honor is bestowed upon individuals or institutions that highlight the goals of CSE, particularly those that improve scientific communication through the pursuit of high standards in all activities connected with editing.

Kerry Kroffe, PLOS’ Director of Editorial Services, accepted the award on our behalf earlier this month at CSE’s annual meeting in Columbus, Ohio.

Photo courtesy of Matt Reese Productions

 

 

 

 

 

 

 

 

 

 

 

Past winners include Annette Flanagin, EQUATOR Network, Ana Marušić, MD, PhD, Amy Brand and ORCID.

We’re heading to NetSci 2019!

Note: PLOS is excited to sponsor the Open NetSci Hackathon and support NetSci 2019.

We can’t wait to see you at NetSci 2019! We’re gearing up for the hackathon (May 25-26) and conference (May 27-31), and want to help you make the most of your NetSci experience. Get ready to meet PLOS staff, tell us the latest research you’re reading, and submit your manuscript to our PLOS ONE Science of Stories call for papers.

Open NetSci Hackathon

Join us for NetSci’s inaugural hackathon. This year’s theme is open code and data, and our CC BY content is made for this! The hackathon will also feature keynote speaker Cassidy Sugimoto and experts on site to help with projects.  

Anyone registered for the NetSci 2019 School and Satellites can join, free of charge, and groups and individual participants are welcome. Learn how to sign up and get involved here.

Chat with us and #shareyourcode
  • Throughout the hackathon and the conference we want you to tweet about any papers, code bases or open code projects using the hashtag #shareyourcode and tagging @PLOSChannels. We’ll feature select works in the PLOS Complexity Channel, curated by Channel Editors including NetSci’s very own Laurent Hébert-Dufresne.
  • At the NetSci conference, PLOS ONE editor Deanne Dunbar will be attending NetSci and will be taking part in the “Chat with the Editors” panel.
  • If you’re a PLOS ONE Academic Editor, we’ll be holding a meet up May 30– email us to attend!
Submit to our call

There’s still time to submit your research to the PLOS ONE Science of Stories call for papers! The call and upcoming Collection include research with diverse perspectives from the humanities and the sciences to:

  • Explore the nature of narrative and narrative thinking in texts and other media.
  • Propose methods to extract stories from datasets and vice versa.
  • Analyze how narratives are transformed and how they cooperate or compete with each other as they move through time and space.
  • Communicate data-rich narratives to the public.

Guest Editors handling submissions are Peter Dodds, Mirta Galesic , Matthew Jockers and Mohit Iyyer. To learn more about our Editors’ perspectives and the call check out their recent blog post. The call is open until June 14.

We look forward to seeing you at NetSci 2019 and wish everyone a great conference!

Mini Frogs and other PLOS Research Making Headlines in March and April!

Mini Frogs and other PLOS Research Making Headlines in March and April!

Five tiny new frog species found in Madagascar–meet the Mini frogs

Three of these five new species, all of which range from 7.7-15 mm in length, belong to an entirely new genus: Mini. These Madagascan frogs’ miniscule scale enriches the picture of convergent evolution towards tininess in frog species (in addition to being extremely cute).

Lead author Mark Scherz says: ‘When frogs evolve small body size, they start to look remarkably similar, so it is easy to underestimate how diverse they really are. Our new genus name, , says it all: adults of the two smallest species Mini mum and Mini scule, are 8–11 mm, and even the largest member of the genus, Mini ature, at 15 mm, could sit on your thumbnail with room to spare.’

Check out some of the media coverage this article’s received from outlets including National GeographicIFLScience and Smithsonian.com, too!

 

(Don’t!) Feel the Burn–SPF moisturizer tends to be applied less effectively than traditional sunscreen

A new PLOS ONE study showed that users applying an SPF30 moisturizer applied it less effectively compared to traditional SPF30 sunscreen users, and missed significant areas around the eyelid. Even more concerningly, a post-study questionnaire revealed that participants were unaware of their incomplete coverage. As we move into summer here in the Northern Hemisphere, don’t forget your eyes need sun protection (and sunglasses are always an option, too!)

Co-author Austin McCormick adds: “Moisturiser is not as well applied as sunscreen; therefore, if planning prolonged sun exposure we advise sunscreen be used. If using moisturiser we advise one with SPF: any SPF is better than none, but it should not be considered the equal of sunscreen.”

For additional summer reading about this PLOS article, head to BBC News, NPR, and Today.com, among others!

 

Climate Change May Contribute to Hay Fever Increase

If you suffer from hay fever, climate change might be contributing to your allergies. A recent study in PLOS ONE showed that areas in the USA where the onset of spring was earlier than normal–or significantly later than normal–corresponded to an increased prevalence in hay fever sufferers. Lead author Amir Sapkota and colleagues used NASA satellite data along with CDC National Health Interview data to compile this first quantitative dataset pointing to a link between spring timing and allergies. The authors speculate that early spring means a longer season for tree pollen, whereas a late spring may mean a high pollen concentration across many different species–in either case, bad news for allergy sufferers.

Sapkota adds: “We need to better prepare, and increase community resilience to minimize the disease burden associated with climate change.”

See more coverage on this paper from outlets including CBS and Ecowatch.com.

 

 

Articles Cited

  1. Scherz MD, Hutter CR, Rakotoarison A, Riemann JC, Rödel M-O, Ndriantsoa SH, et al. (2019) Morphological and ecological convergence at the lower size limit for vertebrates highlighted by five new miniaturised microhylid frog species from three different Madagascan genera. PLoS ONE 14(3): e0213314. https://doi.org/10.1371/journal.pone.0213314
  2. Lourenco EAJ, Shaw L, Pratt H, Duffy GL, Czanner G, Zheng Y, et al. (2019) Application of SPF moisturisers is inferior to sunscreens in coverage of facial and eyelid regions. PLoS ONE 14(4): e0212548. https://doi.org/10.1371/journal.pone.0212548
  3. Sapkota A, Murtugudde R, Curriero FC, Upperman CR, Ziska L, Jiang C (2019) Associations between alteration in plant phenology and hay fever prevalence among US adults: Implication for changing climate. PLoS ONE 14(3): e0212010. https://doi.org/10.1371/journal.pone.0212010

Image captions and credit

  1. An adult male Mini mum, one of the world’s smallest frogs, rests on a fingernail with room to spare. Credit: Dr Andolalao Rakotoarison. CC-BY.
  2. B&W photo; UV photo non sunscreen showing deep dermal pigmentation, a sign of uv damage; UV photo after sunscreen application; UV photo after moisturiser with SPF application (dark areas on images taken with a UV-sensitive camera show SPF protection/coverage). Credit: Austin McCormick et al, 2019. CC-BY.
  3. Sacramento River Bend Outstanding Natural Area. Credit: Eric Coulter, BLM. Public Domain.

 

 

 

It’s Our Preprint Anniversary!

Can you believe it’s been one whole year since we launched our preprint-posting partnership with bioRxiv? This calls for a celebration!

Just last May, we began offering authors the choice of having PLOS post their manuscript to the preprint server, bioRxiv, when they submitted to a PLOS journal*. Our opt-in service has made it easier for authors to post their work early and has encouraged many authors to try preprinting their research for the first time. As of today, we’ve posted more than 2,500 preprints!

Many of our authors have now seen their work go from preprint to published and it’s amazing to see the transformation their work has taken – just take a look at the examples below.

 

Posted

  Published

  Aug 21, 2018 If a fish can pass the mark test, what are the implications for consciousness and self-awareness testing in animals?

  Feb 7, 2019 in PLOS Biology

  June 4, 2018 Precise prediction of antibiotic resistance in Escherichia coli from full genome sequences

  Dec 14, 2018 in PLOS Computational Biology July 2, 2018 Genetically modified pigs are protected from classical swine fever virus

  Dec 13, 2018 in PLOS Pathogens

 

Why we preprint

Whether you’re an author, an editor, or just an avid science reader, preprints offer a lot of advantages for how we share and consume information: they allow research to be shared openly and broadly, spark feedback and collaborations that may not have happened otherwise, enable authors to claim results and demonstrate their work for timely opportunities such as grant proposals and promotions. But if you really want to know how preprints advance science, just ask our authors:


“As statisticians, we provide analysis and data visualization methods for scientists in the field. Sharing code through GitHub and preprints through bioRxiv provides researchers with the latest methodologies as early as possible. The other benefit is that the scientific community can provide researchers with useful feedback prior to publication. This means that we can tailor new methods to scientists’ needs. These interactions were very enriching, and I recommend Open Science to everybody.”

Stijn Hawinkel, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium

A unified framework for unconstrained and constrained ordination of microbiome read count data

 

 

“Publishing a preprint is a great way to get feedback as early as possible from the community. We actually improved the final version of our paper not only based on the great reviews we received from the formal peer review process, but also based on the feedback we learned through Twitter, and other channels.”

Charlotte Herzeel, ExaScience Life Lab, IMEC, Leuven, Belgium

elPrep 4: A multithreaded framework for sequence analysis

 

 

I posted a preprint to bioRxiv when I submitted to PLOS Genetics because I wanted to share our story with scientific community. At submission, I believed we had a complete story that would interest researchers working on various aspects of adhesion biology. I knew that the story would likely develop further after peer review, but I wanted to share the core results with the community.”

Adam Kwiatkowski, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America

Evolutionary rate covariation analysis of E-cadherin identifies Raskol as a regulator of cell adhesion and actin dynamics in Drosophila

 

What’s next

Champagne! But our work on preprints isn’t over yet. We’re experimenting with new ways to raise awareness and interaction with preprint manuscripts through events like live preprint journal clubs, hosted by PREreview, and expanding our preprint offerings to include programs like Preprint Editors on PLOS ONE and PLOS Genetics.We’re also going through ALL of our data on preprints that we’ve collected over the past year to share back to you. Please join us in celebrating this month and stay tuned for more insights into our preprint program soon.

 

*Facilitated posting to bioRxiv has been available on PLOS ONE, PLOS Computational Biology, PLOS Genetics, PLOS NTDs, and PLOS Pathogens since May 2018 and on PLOS Biology since July 2018

We Couldn’t Do It without YOU

Every year, we get to work with new authors, reviewers, and editors who are ushering in the next wave of scientific advancement. We love publishing your work, reading your reviews, and learning from your expertise and we just want to say THANK YOU for supporting PLOS.

Wow, did we really do all of that?

We did! This has been a banner year for PLOS journals. In 2018 we saw more research articles published in PLOS Biology than ever before, began publishing Topic Pages in PLOS Genetics and Benchmarking articles in PLOS Computational Biology, partnered with bioRxiv to post over 1,300 preprints, and committed to moving forward with published and signed peer review. That’s on top of all of the special issues, Calls for Papers, and collections we’ve published in topics ranging from Climate Change and Health to Gender and NTDs.

We’d also like to extend a warm welcome to more than 3,000 new members of the PLOS ONE Editorial Board who have joined us this year to provide more expertise for submission areas that need it most – we’re glad you’re here!

For everything we do at PLOS, we are supported by the dedication of our research communities.

Together, we’re stronger

We are a community of more than 8,000 editors, 65,000 reviewers, and 150,000 authors. When we work together, we can make change happen in scholarly communication. Last year PLOS Pathogens editors hosted six writing workshops to help Early Career Researchers improve their skills and equip them with the tools they need to become authors. We also hosted interactive events like live-streamed preprint journal clubs to bring authors and experts from the community together for real-time feedback on their work.

We’re listening to your feedback from our surveys, event meetups, and Section Calls and want to continue evolving our services in ways that matter to you.

We’re working on new ways for reviewers to get credit for their work through ORCiD as well as signed and published peer reviews. We’re also going to continue the process improvements we’ve started on PLOS ONE to bring a faster, clearer process to our authors along with a number of exciting new options on other journals – stay tuned!

Cite it, share it, celebrate it

For everyone who has contributed to our success this year: our dedicated Editorial Board, incredible Guest Editors, and inspiring reviewers – these articles are for you!

We’re sure we will have many more opportunities to thank you this year but please join us in celebrating your achievements this week by sharing your PLOS contributions with #PLOSCommunity.

Celebrate Open Data Day with Us!

 

Around the world tomorrow groups from all sectors will be celebrating Open Data Day – an annual event that highlights the benefits of open data and encourages the adoption of open data policies in government, business and civil society. As publishers, data availability is crucial for the validation and foundation of new research and key to our mission to help researchers advance the scientific record. In the spirit of Open Data Day, we’ve decided to defer to researchers and data enthusiasts to answer the questions: why is data important and how can we make it better?

We got our answers from Sudhakaran Prabakaran, one of a number of dedicated volunteers at Cambridge University known as the Data Champions who are helping advise members of the research community on managing their data. Read his thoughts below.

Who are the Data Champions? What kinds of data questions do you help researchers navigate?

I think it’s a fantastic forum. [We have] a lot of discussions and people exchange ideas and not necessarily just in the sciences but also in every other field. [Data management] can be kind of confusing, even simple things like can I put my [datasets] in Dropbox? Can I share them in Google Drive? You’re talking about even labeling stuff in desktop computers. There is no clarity because this landscape is fast-moving and people are not trained to catch up with that kind of speed at which things change.

What are you working on right now? How does open data play a role in it?

Our lab thrives on open data. We train machine learning algorithms that looks at specific regions of the human genome and trying to identify the most important mutations and then identify drugs to target them. Most of the datasets I work with people have already published and analyzed those datasets and they’ve extracted what they want. I’m kind of looking at things that they don’t want – I’m looking at non-coding regions, just kind of digging deeper into the datasets.

Why do you think open data is important? What do you think the future open data landscape looks like?

I don’t think open data is enough…it’s the analysis also. For example, we train a lot of machine learning algorithms and in the process we fail many, many times and we know the pitfalls we know what to avoid. But if you share that process with other people that will enable them to overcome it, to get there. It is very difficult and that process can be shared with people.

I think future young people are going to be brought up in an environment where they can just click something and get access to the code and get access to the data themselves. And then the issues of reproducibility would be mitigated if you can share what you’ve done and the data set is there for other people to work with.

What advice would you give to authors and researchers to encourage them to share their data?

I think we have encountered these scenarios even as a data champion in my own department. I think if you if you have incentives, as in [getting] your DOI and authorships for the dataset even before publication then it’s easy to share. It’s your data, [someone] can probably do a different kind of analysis and publish it but they have to cite this data and you will be benefited by that.

And it’s in the best interest of the authors to share it ahead of time because of reproducibility.

 

What can you do to encourage good data management?

You can practice the open data lifestyle by sharing your research data in an open repository and making it available when you submit your manuscript. If you’re reviewing a submission, knowing how to evaluate the associated datasets can be tricky which is why we’ve worked with the Data Champions to cover everything you need to know in this Reviewer’s Quick Guide to Assessing Datasets. If the manuscript you’re reviewing doesn’t have an associated dataset, request it!

About the Data Champions Program

The Data Champions Programme is a network of volunteers who advise members of the research community on proper handling of research data. In this, they promote good research data management (RDM) and support Findable, Accessible, Interoperable, and Re-usable (FAIR) research principles. It is run by the Research Data Management Facility at the University of Cambridge.

 

‘How do we define success?’ – Rethinking failure and success in science

Independent of the context, failure is a word that hardly ever leaves us indifferent. Fear of failure is human nature, and it is common that we prefer not to talk about failures if we can avoid it.  When we think about this in a professional context, failure can have clear and immediate ramifications for reputation and career progression and – as with any other professional – researchers are not immune to this fear of failure

Part of this approach to failure in research is due to the fact that the research system has traditionally rewarded those who are the first to report a finding over those who are second, and those who report a positive result over those reporting a negative one. However, research generally involves a trial-and-error approach and a plethora of negative findings, or protocols that require troubleshooting before they are fine-tuned. Thus ‘failed’ experiments are common; more so than is often recognized or reported. Much effort and many hours of meticulous research endeavour go unrecognized by the current research assessment frameworks, resulting in a considerable squandering of potentially important research outcomes.

The ‘Failures: Key to success in science’ event at the Cambridge Festival of Ideas 2018 aimed to reflect on these considerations in a conversation involving our five panelists and the audience around the notions of failure and success in science.

Our five panellists kicked off the conversation by giving their perspective on what a successful research career should look like.

‘How do we define success?’ asked Cathy Sorbara (Co-chair of CamAWiSE, Cambridge for Women in Science and Engineering), maintaining that science does not have a defined endpoint, that collaboration should be a key part of the research process, and that scientists need to think about how they communicate their work, particularly to those unfamiliar with research. Tapoka Mkandawire (PhD candidate, Sanger Institute) felt that a key aspect of success is to work on something that you feel passionate about and are keen to share. The audience was interested in the forms that communication of research could take and the panellists noted that communication about research should not be restricted to publications, putting forward ideas around visual formats such as videos. Tapoka noted that her research group has developed a comic book to more easily describe their work to children.

A common theme was that the binary classification of success vs failure is somewhat unfair. Should a result be tagged as failure only because it’s negative and not been published? Fiona Hutton (Head of STM Open Access Publishing at Cambridge University Press) advocated the development of a more collaborative open pathway for research, with more openness at all steps of the process, such as that demonstrated with open lab notebooks, to capture the incremental steps that make up the research process. The sharing of negative and null results should be encouraged as well, as a move away from frameworks that rely on impact factors to assess the quality of research; Fiona mentioned DORA as a good initiative in this space, which is gaining support from institutions and funders.

Arthur Smith (Deputy Manager of Scholarly Communication (Open Access), University of Cambridge) and Stephen Eglen (Reader in Computational Neuroscience, University of Cambridge) tackled the challenges with the current research system and acknowledged that this places Principal Investigators (PIs) as the ‘survivors’ of the system, with only a few reaching the top of a steep pyramidal career structure. Stephen stressed that the driving force for getting into research should be a genuine interest in science and not the goal to eventually become a PI. Arthur noted that there are many other career paths available after a PhD and that the skills gained can be used in many other areas, such as the private sector. The training of PhD students should include aspects that go beyond publishing, and should balance this with the development of communication and other skills.

To round up the discussion we asked panellists to provide recommendations for steps that can help shift perceptions about success and failure in science. Here is what they told us:

  • More support for early career researchers, so that they can have an informed, broader view of their career, and of the options after a PhD.
  • Further recognition for the wide range of different roles that scientists play beyond the publication of research findings – for example, peer review activities, mentorship, etc.
  • Provision of credit for recording and reporting troubleshooting, for any work that may not follow the shape of a conventional publication but which would help others engaged in related research.
  • More training for those in a research path, to help them develop a variety of transferable skills, and to recognize the value of those skills.
  • Increased diversity – higher diversity can only be beneficial in driving change towards how success is defined.

Achieving these aims and helping to sway current views about failures in research represents a formidable task, but – much like science itself – change progresses one step at a time and we hope that the engaging conversation at the Festival of Ideas provided one such step to shift how we define “success” in research. As we pursue initiatives towards such change, let’s remind ourselves of Arthur Smith’s definition of success: ‘Success is what makes you happy’.

 

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