The scientific community has historically relied upon publishers for the advancement of science. The publishing community expanded its outlets as new methods of delivering content became available. But communicating science is more than just spreading information. How to realize this in 2014 is a fertile area for creative innovation as compared with 1650.

Some aspects of intelligibility are stylistic, while others are more substantive. On the substantive end, data and method release should be mandatory in a manner that enables rapid reproducibility on the part of the audience. Data storage costs have plummeted [3], so publishers could provide data hosting. Note: we are not talking about adding yet another repository, which many - rightly - feel are already so prevalent they make data more fragmented and less useable. However, there are growing challenges in properly curating data as data size grows. There is also a desperate need to organize the complex and growing amount of associated metadata, which is essential for intelligible data re-use and scientific reproducibility. This seems like an area in which publishers could take a major role. Having a database accessible and operable by a publisher will provide a ‘sandbox’, to organize, make available to reviewers, and build tools for data that are directly linked to specific publications. These data can then be distributed to appropriate community-approved data repositories, or publisher repositories can serve as short-term or (if needed) long-term means to host data types that have no community-approved repository.

Journals should also proactively engage researchers in developing and integrating best practices and standards, and incorporate tools by which the data associated with submitted work can be curated in a user-friendly comprehensible manner.

But reproducibility also requires the ability to manipulate data. Virtual environments like Arvados [4] hold promise for enabling reproducibility of data analysis with versioned scripts and tools. Authors can deposit into a virtual environment the data, tools and scripts they used to manipulate it, and end users can visit the virtual environment and operate on the data. The underlying data should be accessible enough that readers can manipulate analyses while viewing the paper, and see how robust the visualizations and statistics embedded are. One way to counter ‘P-value fishing’ is to make re-analysis so trivial that manipulations would be obvious. The substantive gains would not be limited to conventionally data-rich fields such as genomics. Imagine ‘wet lab’ publications where the article showcases a particular set of gels, but enables the viewing of all results inline through a gallery of alternative gel images. A publication should not be a static display of results and interpretations, but a distillation of the pith of the total scientific activity corresponding to a publishable unit.

An upside of radical transparency for scientists is that it increases the credibility of their work among peers. It is easier to persuade when your audience can see you put all your cards on the table. In computational fields, publishers can add further value by offering benchmarking resources to performance-test tools and methods using standard datasets and metrics. In genomics, performance tests and discussions exist on resources such as GCAT [5] and SEQAnswers [6], and these could be deployed through journal websites. Finally, another benefit of providing more in a publication is that modern technologies can give a sense of what the audience finds of interest. Which figures are being hovered over, which data are pulled, which tables are being rearranged?

Then there is style. Though today some papers arrive with multimedia and interactive features, most do not. Rather, they rely on the toolkit of tables and figures that dates back decades. A paper on the structural features of a biomolecule shouldn’t have figures of beautiful color plates; rather, one should be able to seamlessly view the structure from different angles. Mechanistic interactions should also be illustrated in animated form when necessary and possible. The Walter + Eliza Hall Institute of Medical Research in Australia has produced a set of animations of biological processes [7] that have amassed more than 1 billion views on YouTube. Clearly there is high demand for this sort of presentation. Several journals have already added or are in the process of adding some functionality to their once stagnant figures; for example, the JBC data viewer [8], which allows readers to manipulate imaging data. However, stronger support from the publishing houses, along with more innovation, is needed to provide the best possible reuse of all material in a publication.