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Nicola Romanò boosted
Andrew Jon Thomson

@LianaBrooks excellent points! May I add:

Privilege comes in many shapes and sizes, it’s not all-or-nothing, so you can have various types of privilege without having every possible advantage in life. You can have struggles & suffer injustice and still have privilege in some form. You can have privilege in one area and lack of privilege in another.

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Nicola Romanò

"Freshening up" the material for my course restarting in September.

A lot of my students will be essentially novices... so here is some short Python starting/refresher material! Everything's CC-BY-4.0 so feel free to reuse!

github.com/nicolaromano/BIA4/t

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Nicola Romanò

@tangming2005 Absolutely agree with this. I've recently scrapped a (fairly complex and difficult to interpret) NN pipeline for transcriptomics analysis for a much simpler XGBoost pipeline and performance is the same or higher in all cases.
Also, interpretability is much higher.

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Nicola Romanò boosted
Helena Klara Jambor

‪Looking for literature for review paper:
Is there quantitative data that beauty/aesthetics in charts help user engagement/effectiveness/memory?

#Datavisualization #DataViz #ComputerScience

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Nicola Romanò boosted
Sara Joy :happy_pepper:

Everybody's Free (To Write Websites)

Enbies and gentlefolk of the class of '24:

Write websites. If I could offer you only one tip for the future, coding would be it. The long term benefits of coding websites remains unproved by scientists, however the rest of my advice has a basis in the joy of the indie web community's experiences. I will dispense this advice now:

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Nicola Romanò boosted
fraufriedrich

I can't believe that in 2024 we still have to explain so bluntly that "Academic journals are a lucrative scam". Yet here we are ...
Kudos to the Editorial Board of Philosophy & Public Affairs for resigning en masse and thank you to Arash Abizadeh for explaining why and what's next in the Guardian:
theguardian.com/commentisfree/

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Nicola Romanò boosted
Thorsten Leemhuis (acct. 1/4)

"'With the R515 driver, #NVIDIA released a set of #Linux GPU #kernel modules in May 2022 as open source with dual GPL and MIT licensing. […]

Two years on, we’ve achieved equivalent or better application performance with our open-source GPU kernel modules […]

We’re now at a point where transitioning fully to the open-source GPU kernel modules is the right move, and we’re making that change in the upcoming R560 driver release. […]'"

developer.nvidia.com/blog/nvid

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Nicola Romanò

@dan and the big issue is that even when these things are called out (and I suspect a lot of times they aren't) universities tend to pretend nothing is going on and do as minimum as possible, meaning the person who has been harassed is the one who takes the worst of an already terrible situation

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Nicola Romanò boosted
Albert Cardona

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

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Nicola Romanò boosted
MCDuncanLab

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

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Nicola Romanò

@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?)

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Nicola Romanò

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

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Nicola Romanò boosted
David Eccles 🌻🇵🇸6x🩹🛡️

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.

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Nicola Romanò boosted
Thiago Carvalho

'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

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Nicola Romanò boosted
bioRxiv

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

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Nicola Romanò boosted
Dr Mircea Zloteanu ❄️☃️🎄

#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

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Nicola Romanò

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."

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Nicola Romanò boosted
preLights

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

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Nicola Romanò boosted
Luca Visentin

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

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Nicola Romanò

@b0rk :ablobhearteyes:

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