Nature Research journals trial new tools to enhance code peer review and publication

Starting this month, three Nature journals—Nature Methods, Nature Biotechnology and Nature Machine Intelligence—will run a trial in partnership with Code Ocean to enable authors to share fully-functional and executable code accompanying their articles and to facilitate peer review of code by the reviewers.

 This guest blog comes from Erika Pastrana, Executive Editor for the Nature Research Journals and Sowmya Swaminathan, Head of Editorial Policy and Research Integrity at Nature Research.

Increasing the reproducibility of scientific findings is a goal that all of us in the research enterprise share.

One path towards achieving this is to encourage authors to provide all relevant data and code associated with a published article. This enables others to re-run the analyses, reproduce the results and re-use the code and data to build on the work, advancing science further.

Since 2014 the Nature journals have required authors of studies with custom code or algorithms that are central to the conclusions to provide a “Code Availability” statement indicating whether and how the code or algorithm can be accessed, including any restrictions to access. In 2016, we adopted a policy of mandatory “data availability statements” on all Nature journal papers. The guiding principle is that these statements must provide enough information for readers to be able to reproduce the results and access the code and data for use in their own research.

A number of Nature Research journals have, for years, also peer reviewed code when it is central to the paper to ensure it is vetted scientifically, and provided the code as part of the published paper, typically in the supplementary information or via a link to a folder on GitHub (see this Nature Methods editorial from 2014). Despite our long-running efforts to publish code that is peer reviewed and useful, our platforms have not always been best suited to this task.

We know peer reviewing code is cumbersome as it requires authors to compile the code in a format that is accessible for others to check, and reviewers to download the code and data, set up the computational environment in their own computer and install the many dependencies that are often required to make it all work. To facilitate this process, we recently developed new guidelines for authors and a checklist to help during code submisison—but there are now tools available that go beyond checklists and PDFs.

Code Ocean is a computational reproducibility platform that aims to make code more readily executable and discoverable. The platform, which is based on Docker, hosts the code and data in the necessary computational environment and allows users to re-run the analysis in the cloud and reproduce the results, bypassing the need to install the software.

The trial is optional for authors of papers undergoing code peer review at these selected journals. Reviewers will be offered as much runtime as they need to run the code and analyses (100 hours per month by default), and upon publication, the code and data will be assigned a digital object identifier (DOI) and cited in the article, enabling readers to  access it freely via a link. Code Ocean, through CLOCKSS, will guarantee the preservation of the code, data, results, metadata and computational environment.

By partnering with Code Ocean, we hope to further facilitate compliance with our policies and practices, and to provide benefits to authors, reviewers and readers by improving the peer review experience and facilitating sharing of code that is reproducible and useful. We hope this functionality will also enhance our papers by linking to a platform where the results, code and data can be more easily verified, reproduced and re-used.

We will be attentively listening to the response in our community, and will be surveying all the authors and reviewers that participate in the trial to learn from their experience.

Code Ocean web-based interface

International Women’s Day 2018 – supporting equity in the physical sciences

This guest blog comes from May Chiao, Chief Editor of Nature Astronomy.

In the 1990s when I was studying physics, women were scarce, and it’s difficult to say who complained more about that, the men or the women! Since then, the proportion of women researchers in science has reached 40% or more in the USA, Canada, Australia, Brazil and Western Europe. Notably, Brazil and Portugal are near parity. But most of the women work in the life sciences. In the physical sciences, female representation remains below a quarter.

At Nature Research, the diversity of our authors and referees, not to mention our own staff, is very important. Our physical science journals are striving to find ways improve. From selecting a variety of reviewers (concerning gender, experience, geographic location) to asking those reviewers to expand our pool of our referees, we are constantly trying to reach more people.

To celebrate International Women’s Day today, we offer a collection of articles that highlight gender inequity or promote inclusivity in the physical sciences. We hope they will provide food for thought. And for change.

These articles included in this blog are free to access for a limited time.

Quantitative evaluation of gender bias in astronomical publications from citation counts

Nature Astronomy 1, 0141 (2017); doi:10.1038/s41550-017-0141

Gender discrimination is very much an issue in academia generally and in astronomy specifically. Through machine learning techniques, astronomy papers authored by women are shown to have 10% systematically fewer citations than those authored by men.

Considering climate in studies of fertility and reproductive health in poor countries

Nature Climate Change 7, 479–485 (2017); doi:10.1038/nclimate3318

Factors related to fertility such as population size, composition and growth rate may influence a community’s ability to adapt to climate change, particularly in poor countries. This Perspective describes theories and analytic strategies that can link climate to reproductive health outcomes.

A research agenda for a people-centred approach to energy access in the urbanizing global south

Nature Energy 2, 776–779 (2017); doi:10.1038/s41560-017-0007-x

Urban households in the global south face unique energy access challenges. This Perspective outlines a research agenda based on understanding the needs of urban energy users to promote inclusive urban energy transitions.

Gender differences in recommendation letters for postdoctoral fellowships in geoscience

Nature Geoscience 9, 805–808 (2016); doi:10.1038/ngeo2819

Gender disparities in science are well documented. An analysis of 1,224 recommendation letters from 54 countries for geoscience postdoctoral fellowships reveals that women are half as likely to receive an excellent letter as men.

Rethink your gender attitudes

Nature Materials 13, 427 (2014); doi:10.1038/nmat3975

Unconscious biases are a roadblock for gender equality in science.

Obituary: Mildred S. Dresselhaus (1930–2017)

Nature Nanotechnology 12, 408 (2017); doi:10.1038/nnano.2017.90

Mildred (Millie) Dresselhaus, a pioneer and world leader in nanoscience, passed away on 20 February 2017.

Inequality or market demand?

Nature Photonics 5, 639 (2011); doi:10.1038/nphoton.2011.282

A recent salary survey conducted by SPIE indicates that optics professionals working in North America are likely to earn significantly more than those elsewhere.

Physics for a changing world

Nature Physics 6, 828–829 (2010); doi:10.1038/nphys1830

Fifty years ago, Abdus Salam envisaged a ‘world centre’ for theorists. Now the institute that he founded is adapting to a changing world and to changing ways of doing science.

In addition, Nature Astronomy has published a Focus issue on gender equity: https://www.nature.com/collections/wmzzzfjpyz

Our pick of graphene papers from 2017

Looking back, 2017 was a great year for advances in graphene research. Lightweight and flexible, yet durable, graphene consists of a single layer of carbon atoms arranged in a hexagonal lattice. The material has been used to better solar panel technology, to enhance medical devices, and for the overall benefit of chemical and industrial processes. Nature Research presents a curated collation of graphene papers from our journals’ research portfolio during 2017.

Nature CommunicationsPEGylated graphene oxide elicits strong immunological responses despite surface passivation

Altmetric Score: 172

In the case of cancer treatment, to target specific tumours in the body, researchers have developed techniques where drug molecules are attached directly to the surface of a graphene sheets. Combining the nanomaterial and the drug molecules, these “nanotherapies” could help clinicians treat tumours by transporting the drugs directly to the tumours, where they can be released onto the cancer cells to help fight the disease. The findings are reported in Nature Communications.

Nature Communicationsp-wave triggered superconductivity in single-layer graphene on an electron-doped oxide superconductor

Altmetric Score: 292

Researchers have found a way to trigger the innate, but previously hidden, ability of graphene to act as a superconductor – meaning that it can be made to carry an electrical current with zero resistance. The finding, reported in Nature Communications, further enhances the potential of graphene, which is already widely seen as a material that could revolutionise industries such as healthcare and electronics.

Nature NanotechnologyTunable sieving of ions using graphene oxide membranes

Altmetric Score: 1032

A study published in Nature Nanotechnology describes a graphene membrane that can desalinate seawater, potentially offering easy and accessible potable water globally. The filtration system works by precisely controlling the membrane’s pore size to sieve common salts out of salty water.

NatureRemote epitaxy through graphene enables two-dimensional material-based layer transfer

Altmetric Score: 152

A novel cost-effective method that uses graphene as a “copy machine” to transfer intricate crystalline patterns from an underlying semiconductor wafer to a top layer of identical material is reported in Nature. Researchers worked out carefully controlled procedures to place single sheets of graphene onto an expensive wafer, and then grew semiconducting material over the graphene layer. The findings indicate that graphene is thin enough to appear electrically invisible, allowing the top layer to see through the graphene to the underlying crystalline wafer, imprinting its patterns without being influenced by the graphene.

Nature PhotonicsBroadband image sensor array based on graphene–CMOS integration

Altmetric Score: 247

A paper published in Nature Photonics, describes a method that combines a graphene semi-conductor device with quantum dots to create an array of photodetectors, producing a high resolution image sensor. When used as a digital camera this device is able to sense UV, visible and infrared light at the same time. This is just one example of how this device might be used, others include in microelectronics, sensor arrays and low-power photonics.

Nature CommunicationsGraphene balls for lithium rechargeable batteries with fast charging and high volumetric energy densities

Altmetric score: 246

Researchers have developed a unique “graphene ball”, designed to increase battery capacity by 45 per cent, according to a paper published in Nature Communications. While current research initiatives have advanced the technology behind lithium-ion batteries, these developments must often sacrifice capacity over charging speed, and vice versa.

Nature NanotechnologyUltrahard carbon film from epitaxial two-layer graphene

Altmetric score: 220

A study published in Nature Nanotechnology describes a process for creating diamene: flexible, layered sheets of graphene that temporarily become harder than diamond and impenetrable upon impact. Researchers worked to theorize and test how two layers of graphene could be made to transform into a diamond-like material upon impact at room temperature. They also found the moment of conversion resulted in a sudden reduction of electric current, suggesting diamene could have interesting electronic and spintronic properties. The new findings will likely have applications in developing wear-resistant protective coatings and ultra-light bullet-proof films.

 Nature CommunicationsIntegrated arrays of air-dielectric graphene transistors as transparent active-matrix pressure sensors for wide pressure ranges

Altmetric Score: 151

Researchers have created a three-dimensional, tactile sensor that could detect wide pressure ranges from human body weight to a finger touch. Using highly-conductive and transparent graphene transistors with air-dielectric layers, the sensor can detect different types of touch-including swiping and tapping. Reported in Nature Communications, the apparatus is capable of generating an electrical signal based on the sensed touch actions while consuming far less electricity than conventional pressure sensors.

 

 

Scientific ReportsMulti-frequency sound production and mixing in graphene

Altmetric score: 160

A pioneering new technique that encourages graphene to “talk” could revolutionise the global audio and telecommunications industries, according to a study published in Scientific Reports. Researchers devised a method to use graphene to generate complex and controllable sound signals. In essence, it combines speaker, amplifier and graphic equaliser into a chip the size of a thumbnail.

 

Nature CommunicationsRoom temperature organic magnets derived from sp3 functionalized graphene

Altmetric Score: 540

By using graphene treated with other non-metallic elements, researchers have devised the first non-metallic magnet that retains its magnetic properties up to room temperature, reports a study published in Nature Communications. Such chemically modified magnetic graphene has a vast range of potential applications, particularly in the fields of biomedicine and electronics.

 

 

Chinese New Year | 2018: Year of the Dog

Happy Chinese New Year! 2018 is the Year of the Dog, so we’ve put together a list of our favourite canine-related research papers from recent years. Nature Research invites readers to learn about the effects of domestication in canines, similarities in the genome of ancient and modern dogs, through to how human cardiovascular systems have benefited from their companionship.

Scientific ReportsThe effects of domestication and ontogeny on cognition in dogs and wolves

A study published in Scientific Reports based on where dogs and wolves searched for food after receiving hints, finds our domesticated companions cannot make the connection between cause and effect, but wolves can. The results from this study involving 12 captive wolves, 14 dogs and 12 pet dogs suggest that domestication may have reduced the independent problem-solving abilities of dogs in specific situations.

https://go.nature.com/2Bw1RHo

 

Scientific ReportsBirth of clones of the world’s first cloned dog

In 2005, researchers reported the first dog to be cloned – an Afghan hound named ‘Snuppy’. Since then, hundreds of other dogs have been cloned, offering an opportunity to learn more about the potential benefits and possible drawbacks of cloning animals. A paper published in Scientific Reports describes the creation and clinical follow-up of 4 clones using adipose-derived mesenchymal stem cells from Snuppy as donor cells.

 

 

Nature Communications – Ancient European dog genomes reveal continuity since the Early Neolithic

The genome of ancient European dogs is similar to that of modern dogs, reports a paper published in Nature Communications. The study also suggests Europe was the centre of modern dog evolution, harbouring the oldest uncontested Palaeolithic remains.

https://go.nature.com/2o9zWon

 

Scientific Reports – Dog ownership correlates with lower rates of mortality and cardiovascular disease

Dog ownership appears to be associated with lower risk of cardiovascular disease in single-person households and lower mortality in the general population, reports a paper published in Scientific Reports.

https://go.nature.com/2Eyiq8k

 

Nature Reviews Genetics – Demographic history, selection and functional diversity of the canine genome

Despite being a single species, dogs represent nearly 400 breeds with substantial genetic, morphological and behavioural diversity. Published in Nature Reviews Genetics, this Review discuss how genomics studies of dogs have enhanced our understanding of dog and human population history, the desired and unintended consequences of trait-based selective breeding, and potentially human-applicable insights into cancer, ageing, behaviour and neurological diseases.

https://go.nature.com/2o3h9vC

Scientific Reports – Human attention affects facial expressions in domestic dogs

An initial study published in Scientific Reports suggests dogs produce facial expressions communicatively and increase their frequency based on the attention they receive from another individual. The authors argue that their data points to a more flexible system combining both emotional and cognitive processes in dogs.

An initial study published in Scientific Reports suggests dogs produce facial expressions communicatively and increase their frequency based on the attention they receive from another individual. The authors argue that their data points to a more flexible system combining both emotional and cognitive processes in dogs.

Scientific Reports – Functional MRI in Awake Dogs Predicts Suitability for Assistance Work

Brain scans of canine candidates to assist people with disabilities may help predict which dogs will fail a service training program, according to a study published in Scientific Reports. Data from functional magnetic resonance imaging (fMRI) of 43 dogs provided a modest, but significant, improvement in the ability to identify poor candidates. Despite calm exteriors, some of the dogs showed higher activity in the amygdala – an area of the brain associated with excitability and anxiety. These dogs were more likely to fail the training programme.

 

https://go.nature.com/2EGYHTd

 

If you want to keep up-to-date with research about dogs, why not try Recommended? It’s a free, personalised service that suggests relevant papers to you, based on what you’ve previously read, from all publishers.Recommended

Training to write, submit and publish a scientific paper

Credit: Ludic Creatives

Credit: Ludic Creatives

This is a guest blog from Andrea Aguilar, Publishing Manager in the Nature Masterclasses team at Nature Research. Andrea spoke to delegates in November at SpotOn, an annual conference about science policy, outreach and tools online organised by BMC, Nature Research and Digital Science.

Every year, researchers, science communicators and people interested in science outreach and policies gather to discuss a timely topic in research during the annual SpotOn conference. This year, we convened in the brand-new Crick Institute in London to discuss the tools and skills that make a great researcher.

As part of Springer Nature Researcher Services we were invited to give a lightening talk: five minutes on the different tools that we have developed to help researchers improve crucial skills such as scientific writing and understanding and navigating the publishing system.

The modern researcher needs to be able to absorb the scientific literature and digest it to ask pertinent and relevant scientific questions. The researcher then needs to develop skilful and elegant experimental designs to answer such questions and master scientific writing to produce a good manuscript.

On top of all those core skills, a great researcher also needs to be a good collaborator, peer reviewer, science communicator, mentor and grant-writer. Scientists acquire some of those skills in the lab or their university but such teachings are of variable and inconsistent quality. As a publisher, we can lend our expertise on three specific topics to help train researchers: scientific writing, science communication and, in particular, scientific publishing.

The publishing system is often viewed as a black box that stands between your manuscript and a published article on the linear path to publication.

We think that, actually, the publishing process is one step in a bigger process, in which each step informs the other.

How many times after writing the first draft of your manuscript or your figures have you realised that you actually need an additional experiment or that your scientific question needs to be reframed or refined? Often, writing and building your figures informs your experimental design. In a similar way, the publishing process informs your writing and your bench work through peer-review and editorial feedback.

Understanding the ins and outs of the publishing process can truly empower you to better navigate the system and achieve high levels of publication. Knowing what steps are involved in the publishing process, what the editor expects from you and how to communicate with them through rebuttal and cover letters, and great scientific writing can considerably smooth the process and save you time. Knowing how to be a great peer reviewer and how to communicate efficiently on your research can noticeably lighten your workload and increase your efficiency.

The Nature Masterclasses team was created 5 years ago to help train researchers in all things high level scientific writing and publishing. Over the years, we have developed two types of training: online courses and face-to-face training.

Our online courses on scientific writing and publishing and on the peer review process will teach you through blog posts, videos from Nature Research editors and recognised scientists, and exercises from the comfort of your computer, when you want, where you want.

 

 

 

 

 

 

 

 

You can dip in and out between experiments or complete it in one sitting. You can work in order or make your own order and go back to the course when necessary. No need to wait for your supervisor to get back from a week-long meeting abroad to ask a pressing question about writing a rebuttal letter! A few months ago, we launched a free course on the peer-review process. You just need to sign-up to access it. Do check it out and let us know what you think in the comments.

We also send out editors to deliver face-to-face training to your institution. During these interactive workshops, two editors from our prestigious journals walk you through how to write, submit and publish a research paper and how to work with them through discussions and exercises. The workshops are a great opportunity to chat with our Editors and get one-on-one feedback on a recent unpublished abstract of yours. You can find more information about these face-to-face masterclasses here.

We had a lot of fun at the SpotOn event talking about our trainings. You can find the video here, as well as hear about how researchers are akin to super heroes, what it takes to make a good speech and a lot more in the conference recap.

And finally, a big thank you to the SpotOn team for inviting us to participate this year.