AG JékelyOur Approach to Publication

We believe that radical changes are long overdue in how we publish and evaluate research output.

We support and have fully adopted the Publish, Review, Curate (PRC) (in that order) model. We also believe that we need a publicly-funded open research infrastructure to manage and curate scientific outputs.

We support the new responsible-publishing initiative of coalition S, share the vision of Brembs et al. on the need to replace academic journals (or radically transform them into federated curation platforms) and are excited to see that EU politics is moving in the same direction:

Our lab only publishes in biorXiv, arXiv, psyarXiv (reviews) and Zenodo (code, text and source data as comprehensive and re-usable R projects).

For expert evaluation (peer review) and curation (long-term storage, formatting, promotion), we send our published papers to post-publication peer review services (e.g. eLife) or a few select traditional journals, for example The Company of Biologists, Royal Society or PLoS journals, We also support innovative platforms such as microPublications.

We only work with non-corporate, not-for-profit venues that have contributed to reforming the publication system and are working in the interest of science.

(A few exceptions still remain, including commentary pieces in some corporate journals. These are, however, without any data and we mostly write them to provide lab members with writing experience and improve their CVs).

The model we support centres around the authors and their work. Scientists first publish their paper on a preprint server (it is thus published). They then seek an expert evaluation to assess the strengths and weaknesses of the work. The paper is then curated by a service that ensures the best presentation of the work and the long-term storage of text, code and data. We thus support the new model introduced by Review Commons and eLife, while acknowledging its limitations and that the model will need to be broadly adapted and scaled up to be transformative.

Big shifts are necessary in our thinking to embrace such a new model. The emphasis should be removed from the venue or cover of the paper ("Which journal?") and should be placed on the quality of the work. Publishing should less be about prestige signalling and more about presenting research results with integrity. The impact should not depend on the packaging, but on the intrinsic quality and novelty and also reusability and reproducibility of the work. These criteria should be assessed by a panel of expert evaluators who would also suggest potential improvements or point out flaws in the authors' paper.

The other core aspect of our publishing philosophy is that a paper should be a lot more than a single pdf file and should also include source data, code and reproducible workflows and protocols.

We strive to publish all source data, code and protocols together with the paper. More recently and in the future we endeavor to make most or all figures by scripts rather than graphics programs, and make the entire workflow available as fully reproducible R projects. We believe that in publishing, the complete presentation of source data and computational workflows is equally important than presenting text and figures.

For an example, please see our recent paper describing a new function of nitric oxide signalling in UV-light-avoidance in Platynereis (the GitHub page is here).

Or this paper reporting the discovery of the neuropeptide ligand for 31 cnidarian GPCRs. For this paper, we used an accompanying and citable code and source data repository.

All prospective PhD students and postdocs wishing to join the lab will have to agree to this policy. You may think that this takes away some basic freedom to choose where you send your paper, but in our experience it gives you a lot more freedom to focus on your work and write your paper as you think it is best (not to fit some journal's expectations). This approach also reduces publishing anxiety and stress and the drive to overinterpret results and overstate significance. And you can still publish awesome papers!