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March 18, 2014 / Damien Irving

The future of journal submissions

Recent advances in computing and the web have revolutionized the way we do weather/climate science. For instance, a computer model that took a year to run a decade ago can now be run in 30 seconds, meaning we can conduct analyses and produce volumes of data that were previously unimaginable. We can also share these data and analyses faster than ever before, through both traditional (e.g. early online access to journal papers) and non-traditional (e.g. social media, blogs) mediums.

In contrast to these rapid advances in the way we conduct and share science, there has been relatively little change in the way we publish science. Journal articles are obviously now available online, however the criteria against which they are reviewed and the format in which they are presented has remained relatively unchanged for decades. This situation is to be expected to some extent, because the natural sequence would be for science to change and then publishing to adjust accordingly. Indeed, in recent years topics such as reproducibility and open access have dominated the editorial sections of Nature and Science, so it appears that change is on the way.

With this imminent change in mind, I thought I’d consider what journal submission might look like 10-20 years from now in the weather/climate sciences.

 
Copyright / access

The push for open access has grown rapidly in recent years, with some of the most influential political and academic institutions calling for change. The White House recently announced that taxpayer-funded research should be made free to read after a years’ delay, while Princeton University have established a policy that prevents researchers from giving the copyright of scholarly articles to journal publishers. Everyday scientists are also screaming for change, with thousands boycotting publisher Elsevier due to the exorbitant fees they charge for access to scientific publications.

All this means that in 10-20 years from now, manuscript submission probably won’t involve signing one of those forms that gives copyright to the journal. It’s also likely that your paper will be openly available from the moment it’s accepted, or will at the very least become open access after a short delay (e.g. 12 months). While this is great news for readers, it seems that authors will still be charged a fee to have their work published. PLOS journals currently publishes some of the highest profile open access journals going around, and they cover costs by charging authors a fairly hefty fee (ranging from about $1,000 to $3,000 depending on the discipline).

 
Source code, data and other supplementary material

A major consequence of the recent advances in computing is that published research is becoming less reproducible. For instance, Nature recently published a series on the challenges in irreproducible research, which included an article outlining the case for open computer programs. This culminated in substantive changes to the checklist reviewers must consider when assessing a Nature article. Particularly relevant to the weather/climate sciences is that this new checklist encourages “the provision of other source data and supplementary information in unstructured repositories such as Figshare and Dryad.” It also asks whether “computer source code was provided with the paper or deposited in a public repository?”

In a nutshell, Dryad is a website where you can make your data publicly available, while Figshare is a place to share all sorts of things that can’t be included in a traditional journal paper (i.e. not only datasets but also supplementary figures, media, papers, posters, presentations and filesets). The great thing about these sites is that your data/materials get a Digital Object Identifier (DOI), so that they can be uniquely cited by others. PLOS recently annouced that authors must make all data underlying their findings fully available without restriction (with rare exception), so if journals in the weather/climate sciences follow suit then in 10-20 years time this sharing might actually be compulsory.

With respect to source code, it’s not difficult to imagine that in 10-20 years time all weather/climate journals will require authors to make their code available upon submission. In fact, the Mozilla Science Lab are currently midway through the second iteration of a project to figure out how peer review of scientific code would actually work. They’re also working on making it possible to push code from GitHub (a commonly used code repository; see my post on version control for details) to Figshare, which would allow scientists to get a DOI for their code as well.

 
Methodology

In the announcement of the new Nature checklist, it was also noted that the journal will now be demanding more precise descriptions of statistics, and will commission statisticians as consultants on certain papers at the editor’s discretion and at the referees’ suggestion. In other words, it’s conceivable that in 10-20 years time journals may demand a far more detailed description of the research methodology.

 
Peer review process

If the new open science journal F1000 Research is anything to go by, we can also expect that the peer review process might be more open and transparent in 10-20 years time. Articles submitted to F1000 are published immediately, then reports from reviewers (along with their names) are published alongside the article as they become available, together with comments from registered users. In the case of other more typical journals (i.e. with a slow and closed/private review process), this desire to publish immediately is leading researchers to post their articles on pre-print servers like arXiv, so that their work is available to the wider scientific community while it’s being reviewed.

 
Rather than waiting to get caught out by these changes to the journal submission process, why not get ahead of the game? If you’re submitting a paper soon, consider making your code available on GitHub (or even RunMyCode.org) and your data available at Dryad. Alternatively, if you’re reviewing a paper, why not suggest to the author that they do the same?

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4 Comments

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  1. Damien Irving / Mar 21 2014 14:34

    An update on the Mozilla Science Lab “code as a research object” project can be found here: http://mozillascience.org/code-as-a-research-object-updates-prototypes-next-steps/

  2. Stewart / Apr 9 2014 12:35

    “a computer model that took a year to run a decade ago can now be run in 30 seconds”.

    Not only that, a computer model that took a year to run a decade ago on a mainframe computer can now be run in 30 seconds on a personal laptop computer.

    I wonder if there is a Moore’s-like law pertaining to computer size?

  3. Matthias Tomczak / Apr 28 2014 12:38

    You don’t have to quote a journal from the life sciences (F1000RESEARCH) to promote the model of immediate publication, open publication of reviews and authors’ answers, inclusion of comments from others, and personalised copyright under the Creative Commons Attribution Licence. The European Geosciences Union publishes 14 journals under that model, including Atmospheric Chemistry and Physics, Atmospheric Measurement Techniques (e.g. remote sensing), Earth System Dynamics, Ocean Science (where I have published since 2006), The Cryosphere, and others. All journals also allow the deposition of additional material. If you want to get your work out immediately and have it reviewed openly rather than through a secret process consider publication in one of EGU’s journals: http://www.egu.eu/publications/open-access-journals/

    • Damien Irving / Apr 28 2014 12:49

      Thanks, Matthias! I wasn’t aware that their process was quite so open and progressive. I think I might target one of the EGU journals for my next publication…

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