Nicola Romanò @nicolaromano@qoto.org
Senior lecturer at the Zhejiang-Edinburgh Joint Institute (ZJE) and Edinburgh University.
Undergraduate Programme Coordinator, Biomedical Informatics at ZJE.
I teach #imageanalysis & #dataanalysis with #RStats & #python. I study #heterogeneity in #pituitary (and other) cells.
I'm also very interested in #reproducibility and #openscience.
Joined Oct 2022
Nicola Romanò
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Optimizing murine sample sizes for RNA-seq studies revealed from large-scale comparative analysis https://www.biorxiv.org/content/10.1101/2024.07.08.602525v1?med=mas
Nicola Romanò
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#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
"Rodent chronic variable stress procedures: a disjunction between stress entity and impact on behaviour"
https://www.biorxiv.org/content/10.1101/2024.07.04.602063v1.full.pdf+html
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."
#chronicVariableStress #stress #reproducibility #ethics #effectSize #translationalResearch #physiology
Nicola Romanò
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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 👉 https://prelights.biologists.com/highlights/an-analysis-of-the-effects-of-sharing-research-data-code-and-preprints-on-citations/
#sharing #preprints #code #data # collaboration #science #ResearchCulture
Nicola Romanò
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I cannot stress enough how good the Atkinson Hyperlegible font is: https://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?
Nicola Romanò
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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👇
http://arxiv.org/abs/2302.07005
Reboosts appreciated
Just finished my first test using #shiny with #python!
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
https://apps.nicolaromano.net/BitDepth/
And code here, feel free to modify/reuse at will!
https://github.com/nicolaromano/BIA4/tree/main/Apps/BitDepth
Do you use anything similar? Do you find it effective?
Nicola Romanò
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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.
Nicola Romanò
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#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
Nicola Romanò
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#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🤝🚀
https://www.biorxiv.org/content/10.1101/2024.04.19.590278v3
Nicola Romanò
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“If you thought that science was certain - well, that is just an error on your part.”
― Richard P. Feynman
Nicola Romanò
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🌟 Exciting news! Just a week to go until #SciPy2024! 🎉 Stay tuned over the next few days as we reveal some of the amazing things our speakers will be presenting at the conference 👀
Nicola Romanò
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"But whilst it will have its benefits, the process of datafication also raises important methodological and ethical questions. Who has access to the data that is collected and why? How do the new data flows change everyday research practice? Are scientists being subjected to “dataveillance”, and if so, what does this mean for their privacy? To ensure that the scientific community embarks on a critically informed journey towards a datafied research ecosystem, these questions need to be addressed."
https://www.embopress.org/doi/full/10.1038/s44319-024-00153-2
Nicola Romanò
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“On AI and the commoditisation of design – Scott Riley”
https://www.scott.is/writing/about/ai-and-design
> That’s because I know the value good design can bring to a project, and it’s not the output. Design is about humans, about sense-making, systems thinking, and craft
Nicola Romanò
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« In this Comment, we emphasize the complexity of scientific software as a multifaceted socio-technical (and historically grown) system. We describe facets of software that we define as vantage points from which the different dimensions of software can be understood. The multifaceted nature of software implies that the work done by software has technical, legal, sociological and epistemic consequences. »
Nicola Romanò
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appreciated this essay about “technical” skills by Sasha Laundy (“If you've ever said "soft skills" and felt weird about it, this essay is for you”) https://sashalaundy.com/writing/technical-skills/
Any Shiny for Python experts out there? I'm starting to play around with it; I've deployed my app to a DigitalOcean droplet running Shiny Server and pointed /etc/shiny-server/shiny-server.conf to a venv I want to use.
That works like a charm, but I'm wondering if I would be able to use multiple environments in case I wanted different apps to use different package/Python versions. Not a deal-breaker (and honestly I don't have a use case right now, but still...)
Senior lecturer at the Zhejiang-Edinburgh Joint Institute (ZJE) and Edinburgh University.
Undergraduate Programme Coordinator, Biomedical Informatics at ZJE.
I teach #imageanalysis & #dataanalysis with #RStats & #python. I study #heterogeneity in #pituitary (and other) cells.
I'm also very interested in #reproducibility and #openscience.
Joined Oct 2022
