First preprint + research compendium + data sharing

Excited to announce the first Lab preprint manuscript posted on bioRxiv 1 accompanied by a research compendium, - in our case a GitHub repository structured following a convention to organize all files produced during the research such as raw data and R scripts used for analyzing the data and producing the plots. I found important to prepare a website to facilitate visualization and understanding by the interested reader or reviewers of the manuscript by reading a better documented analysis.

I was wondering about all benefits from posting on a preprint server (beyond producing and storing a PDF) when we are able to prepare our own preprint versions (HTML or PDF) and post in a repository (e.g. GitHub) together with the research compendium. I had insightful feedback on Twitter by top experts in reproducible research:

OK! much clear now. Next step would be a decision of which preprint server to use. I was informed that either of the two most common in the life sciences would be great options. I decided for the most traditional one, where preprints seem to get more attention and views, but I will use PeerJ next time.


As to data sharing, although the raw data can be obtained from the GitHub repository, they were permanently stored at the Open Science Framework (OSF) server and can be cited as:

Del Ponte, E. M. 2017. Fitness traits of deoxynivalenol and nivalenol-producing Fusarium graminearum species complex strains from wheat. Available at: osf.io/7v4ht.

I am tracking statistics on the number of visualizations and downloads, which is nice feature besides the ones commented above. The manuscript has been submitted 🙌 and is currently under review. Once it is (hopefully 😃) accepted, I will be able to update and upload it to biorXiv server so those with no access to the paywalled version can read it.

By the way, this manuscript is an outcome of an MSc research conducted by Camila Nicolli to increase our understanding about the biology and ecology of fungal strains representing different members of the Fusarium graminearum species complex. These fungi are the main cause of Fusarium head blight, a damaging diease in small grain crops and a focus of our research in the lab during the last 15 years.


  1. ”..authors use the bioRxiv service to make their manuscripts available as “preprints” before peer review, allowing other scientists to see, discuss, and comment on the findings immediately. Readers should therefore be aware that articles on bioRxiv have not been finalized by authors, might contain errors, and report information that has not yet been accepted or endorsed in any way by the scientific or medical community. Source: bioarXiv ^

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