Show me the data!

Brockington Lab Weekly Research Round-Up

July 13th, 2016 | Posted by rmounce in Publications | University of Cambridge - (Comments Off on Brockington Lab Weekly Research Round-Up)

This week I chose the papers for the Brockington Lab ‘journal club’ here at the Department of Plant Sciences, University of Cambridge (I prefer to call it the ‘weekly research round-up’ though, because good content has nothing-to-do with journals per se!).

We rotate the choice of papers between each lab member every week. Sometimes the focus is betalain or cuticle research, but every 3rd week the focus is on broad-interest research.

The three papers I picked this week are all super-interesting and have a common theme: open research!

1.) Islam et al. (2016). Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae bioRxiv DOI: 10.1101/059832

2.) Erin C McKiernan, Philip E Bourne, Titus Brown, Stuart Buck, Amye Kenall, Jennifer Lin, Damon McDougall, Brian A Nosek, Karthik Ram, Courtney K Soderberg, Jeffrey R Spies, Kaitlin Thaney, Andrew Updegrove, Kara H Woo, & Tal Yarkoni (2016). How open science helps researchers succeed eLife DOI: 10.7554/eLife.16800

3.) Eklund, A., Nichols, T. E., and Knutsson, H. (2016) Cluster failure: Why fMRI inferences for spatial extent have inflated false-positive rates. PNAS DOI: 10.1073/pnas.1602413113


Paper 1

Paper 1 by Islam et al. is what we spent the most time discussing. The Open Wheat Blast project came to my attention a few months ago via Nature News. It’s really good to see such a globally-involved multi-author collaboration where all the authors have ORCIDs, posting a preprint before the journal submission AND making all the data openly available as it happens. I won’t say too much but we did have some questions over the science of the paper — was it really necessary to do full scale transcriptomics/genomics to identify the possible origin of the pathogen? We’re not experts in plant disease but could less expensive, more targeted nucleotide sequencing approaches have given the same phylogenetic results?

Paper 1 was also made available online at a preprint server which gave me an excellent opportunity to explain what a preprint server was to the group. I even tried to give an account of possible ‘negatives’ of preprinting: the only one I could think of was embarrassment if the work was demonstrably incorrect or obviously messy/unfinished (but who would actually do that?).

It was also fun to read and analyze a paper in it’s unformatted state. This is what a paper looks like at submission before the imposition of a 2-column layout, journal branding, logos and other crap.


Paper 2

screenshot of the 'How open science helps researchers succeed' paper














It was my delight to see ‘How open science helps researchers succeed’ get published in eLife the week before the research round-up meeting: perfect timing! We didn’t get much time to discuss it but I hope our group read it. It’s a really solid review of how open research practices can help the individuals doing open science, not just ‘sacrificially’ helping others, as people sometimes tend to cynically interpret it. I was tempted to also suggest the recent opinion paper ‘How publishing in open access journals threatens science and what we can do about it‘ but it’s such a poor quality paper with so many glaring factual errors (there’s an excellent post-publication review on Publons) I didn’t even bother to send it round the group.

Paper 3

Again we didn’t get time to discuss this in detail but I was really pleased that Caroline our visiting undergraduate from Oberlin College had read about this one even prior to me selecting it for our weekly round-up. It’s had a heck of a lot of media coverage (deservedly!), and we hope to talk about it in depth at one of the next OpenCon Cambridge meetups — there’s been some useful discussion of it over on the OpenConCam mailing list. You might think it weird to suggest a neuroscience fMRI paper in a plant sciences group – but the relevance isn’t about the study system. It’s the fundamental need for data archiving, and statistical rigour that are demonstrably important here and it’s a lesson for all disciplines not just neurosciences.


In about seven weeks time it’ll be my turn again to choose the papers. It’ll be hard to top those three papers for awesomeness though! Well done to all the authors for the great work.