Advantages of submitting first to the @biorxivpreprint : as an editor, I can share the entire paper with prospective reviewers to entice them to review it.

Let me tell you: this is a massive deal. Finding reviewers willing to commit to submit a review "soonish" (less than 2 months) is becoming tough.

#ScientificPublishing #academia #preprints

I'm thinking about the FAIR (findable, accessible, interoperable, and reusable) principles of data. Much of our data is Western blots. Amongst colleagues, we were discussing how hard it would be to make it 'findable' which would require metadata schema, but I'm reconsidering it now.

I found a German paper from 2015 that has not really been cited and is more theory than practice. I wonder if anyone is actively working on this?

I'd be happy to participate.

#Opensource #metadata

@Mehrad That's odd, I never encountered any problems with Fedora (I'm currently running 39, is it possible that 40 is so much worse?)

@cyrilpedia you got to appreciate this little gem . I'm assuming an aptronym, but could be a zombie...

I've been made redundant from my job, effective tomorrow.

So... if you know anyone who's in need of a bioinformatician to work remotely on small bioinformatics projects, please let me know.

'Correlation is not causation: this simple and uncontroversial statement has far-reaching implications. Defining and applying causality in biomedical research has posed significant challenges to the scientific community. In this perspective, we attempt to connect the partly disparate fields of systems biology, causal reasoning, and machine learning to inform future approaches in the field of systems biology and molecular medicine'

embopress.org/doi/full/10.1038

Optimizing murine sample sizes for RNA-seq studies revealed from large-scale comparative analysis biorxiv.org/content/10.1101/20

#statstab #132 P-Values are Random Variables

Thoughts: Ever-confusing, p-values are the bain of intro research method students. Maybe simulation is the key.

#stats #education #pvalues #NHST #simulation #edutstadon
#psychology #statistics

jstor.org/stable/27644033

New on !

"Rodent chronic variable stress procedures: a disjunction between stress entity and impact on behaviour"

biorxiv.org/content/10.1101/20

We systematically investigated 350+ studies using chronic variable stress procedures in rodents and assessed the characteristics of the procedure (how many stressors they used, and how many different types, and for how long), then measured the reported effect size for those using behavioural tests as an outcome.

Some key disconcerting findings from our study

- the large majority of articles uses a unique protocol, and articles featuring the same protocol were from the same authors (aside from one case)
- 91% of articles don't provide any justification for their choice of procedure

This is scientifically and ethically troubling given CVS procedures deliberately impose suffering to animals.

- when looking at the outcome behavioural procedures measured in the studies (some of which impose further stress on the animals) we found very little correlation between effect size and the characteristics (eg length, strength) of the stress protocol. When there was a statistically significant effect, this was generally very small.

We conclude

"Most of the studies in our review sought evidence for interventions that would prevent or reverse the effects of chronic stress. But if we are to have any confidence that translational CVS studies provide a foundation for potential clinical interventions, we must take an evidence- and ethics-informed approach to their design."

Sharing is caring!

#OpenScience practices (e.g. preprints) increase the impact of research articles as measured by citations. #preprint from Giovanni Colavizza and colleagues.

#preLight prepared by Priyanka Pant, Katarzyna Lepeta, Shalini Roy Choudhury & Reinier Prosee

#preLight 👉 prelights.biologists.com/highl

#sharing #preprints #code #data # collaboration #science #ResearchCulture

I cannot stress enough how good the Atkinson Hyperlegible font is: brailleinstitute.org/freefont

It's very pleasing on the eyes and it helps everyone understand and read your text, plus - it's completely free, even for commercial purposes!

What's not to love?

#accessibility #fonts

Reproducing bioimages and data analysis is a problem in the scientific world. No guidelines on how to do this, nor do journals have any recommendations for authors, until now! We have teamed up from around the world and developed a checklist to help make science reproducible👇

arxiv.org/abs/2302.07005

Reboosts appreciated

Just finished my first test using with !

I am thinking of creating a few of these for my image analysis course (because there is not enough stuff to do already 🤣)

Here it is

apps.nicolaromano.net/BitDepth

And code here, feel free to modify/reuse at will!

github.com/nicolaromano/BIA4/t

Do you use anything similar? Do you find it effective?

Basically I feel a little silly even posting this, because to me it's obvious. It's like there is a big red button that says "Fascism" and I'm like "do I really need to say that I think pushing that button is a terrible idea?"

But just in case? Under no circumstances should we push the big red button.

Elect Biden again and proceed to make him *miserable*

Better than being too miserable to get anything done.

Show thread

#Introduction Hello. I'm a law prof, a philosopher, a progressive. I've deactivated #twitter and am searching for a new place to learn and to think out loud. #politics #law #democracy #elections #art #literature #history #science #books

@Brokar @natematias I guess a lot of people would notice, given how much Airbnb is used... Not saying it's necessarily a bad idea, but I doubt it's the solution to the housing crisis

#preprint alert 🚨
Can Large Language Models solve common #BioImageAnalysis coding tasks? And which #LLM performs best? 🙃🤓
Great collaboration with Christian Tischer, Jean-Karim Hériché and Nico Scherf
🔬🖥️🅰️ℹ️🤝🚀
biorxiv.org/content/10.1101/20

“If you thought that science was certain - well, that is just an error on your part.”
― Richard P. Feynman

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