I am giving a talk next week and wanted to update some plots from an old analysis that previously featured on quantixed. The question is: how long does it take for a paper get published? The answer is complex (as previously discussed on quantixed), but we can at least find out using data from PubMed what journals declare as the time from when a paper is received to when it was published. The code is below and can be found here.

When a preprint is uploaded to bioRxiv, it undergoes screening before it appears online. How long does it take for Affiliates to screen preprints at bioRxiv? tl;dr I used R to look at bioRxiv screening times. Even though bioRxiv has expanded massively, screening happens quickly (in about 24 h). I am a bioRxiv Affiliate – one of the people who does the screening. Preprints wait in a queue to be screened.

I’m posting this the morning after generating a graph, and it’s already out-of-date. During the worldwide COVID-19 outbreak, preprint servers such as bioRxiv and medRxiv have again shown that they are the most effective way of communicating science rapidly. A collection of all papers on COVID-19 deposited on these two servers is available here, and it is growing daily.

So this is essentially what happened instead of us sitting down and thinking how we could spend our money in the most technologically savvy way to the benefit of science, scholars and society. A generation later, roughly US$300 billion poorer and none the wiser, it seems.

I run a Masters module called MD997. Over six weeks, students have to write a grant proposal and then assess their peers’ proposals at a mock grant panel. Each student bases their proposal on a paper. They present that paper to the class and then they write their proposal using the paper as a springboard. I refreshed my paper list this year to consist of solely papers published (or posted on bioRxiv) in 2019. The previous list is here.

This is the last blog post of 2019 and it is time again to look back at some of the amazing research published in GigaScience over the past year. Besides handling manuscripts, reviews and data, the editors and curators also attended conferences near and far, they contributed to policy discussions and prepared the launch of a new journal, GigaByte. More about all these activities below.

For a number of years now, publishers who expect losing revenue in a transition to Open Access have been spreading fear about journals which claim to perform peer-review on submitted manuscripts, but then collect the publishing fee of a few hundred dollars (about 5-10% of what these legacy publishers charge) without performing any peer-review at all.

As part of the FAIRsharing Community Network (see previous blog) and joint Force11 and Research Data Alliance (RDA) FAIRsharing Working Group we have been involved in efforts to develop a shared, cross-publisher list of recommended data deposition repositories. The first fruits of these are a preprint from the working group and DataCite (of which we are also members) summarising what we feel should be the key criteria for selection.

This is a follow up to a previous post. Despite what the title says, it is what we wanted. Our paper on dongles has just been published in Journal of Cell Science. The previous post on quantixed , explained all about the paper and the background to it. The journal featured our paper as a research highlight and they also interviewed first author, Cansu Küey.

We have a new paper out! You can access it here. The paper in a nutshell We have discovered a new class of trafficking vesicle inside cells. These vesicles are very small (30 nm across) and we’ve called them intracellular nanovesicles, or INVs for short. What is a trafficking vesicle? Humans are built from lots of cells.