Nicola Romanò @nicolaromano@qoto.org

🔖 Statistical code in a high-impact medical journal

A journal started asking authors to submit code with their manuscripts. They then analysed the next 314 papers accepted

87% denied using code, even when publishing substantial statistical analysis

10% used code but refused to share it with the journal

For the few that provided code, none scored even moderately on basic quality criteria

Assel & Vickers
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6705117/

#MedMastodon
#OpenScience
#ResearchWaste
#doi:10.7326/M17-2863

Thanks to a toot from @DavidKnuffke that I saw this morning, I tried another #AI tool - Elicit https://elicit.org/
"This workflow tries to answer your research question with information from published papers."
My example is shown here with my initial question in the red box. Wow.
#EdTech #EduTooter #Education #GoogleEDU

Just making sure that the Mastodon #rstats community is aware of the {dadjoke} package. And if you need it, add this to your .Rprofile for a dadjoke on startup:

# Dadjoke on start up
if (interactive())
dadjokeapi::groan(sting = FALSE)

🔖 Do cancer researchers make their data and code available?

306 cancer studies:

16% shared data

4% shared analysis code

1% of data were FAIR (posted to a recognised repository, in a non-proprietary format, with an identifier and a license)

Cancer research transparency was this bad despite many journals having policies mandating openness.

Daniel Hamilton et al
https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-022-02644-2

#MedMastodon
#OpenScience
#ResearchIntegrity
#ResearchWaste
#doi:10.1186/s12916-022-02644-2

@Sheril
Im in my 50s. When i was in school, i wanted to study sharks. I was told no women made contributions to science (cept Currie, who they could not ignore, though they tried!). And it was because THERE WERE NO WOMEN IN SCIENCE, and not because “women were there, but we dont learn about them!”

I hope no other 10 year old decides to go into a field she doesnt want, because aomone says she cant do what she really wants to do.

In 1925, Dr. Cecilia Payne completed her PhD thesis, described as “the most brilliant ever written in astronomy.” At a time when few #women entered academia, Payne discovered what the universe is made of. Her work began a revolution in astrophysics.

Dr. Payne-Gaposchkin became the 1st female professor & 1st female department chair at Harvard. Given most of us remember names like Darwin & Newton, we should also celebrate Payne. #science #space

Read more at https://www.aps.org/publications/apsnews/201501/physicshistory.cfm

Using ALT to describe pictures and photos is actually much more tricky than it sounds - it’s not about making a jokey comment but trying to use words to reflect an image. Sometimes you discover new aspects to the image and why you. chose it, too

Expansion microscopy is one of the best things to come along in #cellbiology. A new preprint from Ons M’Saad in the Bewersdorf lab at Yale describes methods for ~8000-fold volumetric expansion and labeling that deals with the dilution problem associated with such huge expansion. Cell-level details can be observed with a cell phone camera!

https://www.biorxiv.org/content/10.1101/2022.11.29.518361v1

Fellow academics:

Strongly consider changing your syllabi now, and designing assignments that can't be fulfilled by #AI chatbots. Even better, consider only assigning work that students will actually be excited to do themselves (for instance, autobiographical essays).

I just got OpenAI to write a better essay on #minstrelsy & US #popmusic than most of my UG students could muster, in about 1 second.

A new version of our "Current state of #singlecell #proteomics data analysis" pre-print is available on #arXiv.

We compare the computational workflows used over the last four years and identify a profound lack of consensus on how to analyse SCP data. There's a clear need for benchmarking, standardisation, and better experimental designs. We cover the current standardisation efforts, list remaining missing pieces, and conclude with lessons learned from replications.

(1/2)

Neuronal growth cones from neurons isolated from a giant sea slug (Aplysia californica) photographed through a microscope. #CellBiology #CellBio2022

Mondrian Crescent

I love it when train doors align at the end of a tunnel. The red tiles at Green Park station make this the ideal location to capture this moment.

It wasn't luck though, instead I froze the moving train with a fast shutter. It took ages to get it centred.

This final image resembles an abstract art painting by Piet Mondrian.

#art #mastoart #abstract #architecture #photography #potd #symmetry #london #underground #londonunderground #railway #mondrian #tiles #photo

BEHOLD

I have survived another year despite the machinations of my haters, which can mean only one thing:

It's time to BATTLE SOME JAMS

Welcome to the Third Annual

"24 Days Until December 25th"

Ranking of the Entrants in the Bonne Maman Non-denominational Calendar of Jams!

#jamvent