Nicola Romanò @nicolaromano@qoto.org

@nicolaromano Exactly! The specific language is less important than the ability to write dependable and understandable code. R wasn't developed as a general purpose programming language and it's not fair to judge it that way (Python on the other hand...). Even then, the R community adapted the language and practice to better support making standalone applications, to make documentation and testing easier, etc. There's at least movement in a good direction. Excel just keeps adding less and less useful features without addressing any of its core shortcomings. Excel doesn't improve, it just gets bigger and its UI keeps churning.

It's only Monday and I'm already done with this week. I watched a work issue turn increasingly acromonious over either miscommunication, misunderstanding procedure, or being too wed to a tool to admit it's problematic. I drafted about half a sentence in chat, then stopped because I didn't think I was adding anything necessary and didn't want to make conflict any worse.

I'm increasingly convinced that Excel spreadsheet files should self-destruct or become permanently read-only after 90 days. That's plenty of time to migrate data into a proper database or to migrate calculations into a programming language amenable to auditing, verification, and change control. Excel should be treated as an attractive hazard with a time limit on how long an unverifiable and hostile-to-revision-control worksheet should be suffered to live.

Sadly, these two thoughts are related. Spreadsheets in their current form are too dangerous to be used for engineering work.

I finished my summer internship this week! I spent 4 months working with a team of biologists and statisticians at The Jackson Laboratory, building visualization software for their research needs. The lab I worked with focuses on analyzing genetics, the microbiome, and addiction-related traits. Here's an overview of some of the EDA tools I built for them in #Python ☺️ #genetics #biology #addiction #dataviz #computerscience #research #phd

If you're doing cool work with data vis + bio, lmk!

Black hat hackers demo keycard vulnerability in millions of hotel rooms worldwide:

"They merely tap those two cards on a lock, the first rewrites a certain piece of the lock's data, and the second opens it."

Interesting read. Time to change the hotel lock tech? Again?

https://www.wired.com/story/saflok-hotel-lock-unsaflok-hack-technique/
#Security #Hacking #Travel

A small rant about zombie ideas and the tendency to keep looking for modifications of study methods to avoid concluding that a null result is really null. http://deevybee.blogspot.com/2024/03/just-make-it-stop-when-will-we-say-that.html
#research #nullresults #laterality #handedness #publicationbias

I've been writing serverside SQLite applications for several years now and I still picked things up from this article, which is extremely good. https://kerkour.com/sqlite-for-servers

@futurebird Someone once told me "It's not Kafkaesque to wake up an insect. If you wake up an insect and your first thought is that this might make you late for work...*that* is Kafkaesque." That completely changed my perspective on a lot of things.

Excellent piece from Grégory Miras on why new tools that change #accents in real time are harmful and problematic - they erase diversity - and make us less able to appreciate and listen to that diversity.

#linguistics #AccentBias

https://theconversation.com/why-ai-software-softening-accents-is-problematic-197751

Metrics reloaded. "A comprehensive framework guiding researchers in the problem-aware selection of metrics."
A must-read for everyone doing #ImageAnalysis in #biology
https://arxiv.org/abs/2206.01653

One of the largest science funders, the Bill & Melinda Gates Foundation, will cease paying journal “article processing charges” and instead asks funded researchers to publish their work as preprints. This is fantastic. The costs of the current publishing system drain research funds and exclude too many scientists solely due to financial constraints. Funders are in a much better position to rock the “publishing” boat than researchers.
https://gatesfoundationoa.zendesk.com/hc/en-us/articles/24810787662100-Policy-Refresh-2025-Overview

#academia #OpenScience #research

Have to output a bunch of dense scatterplots to PDF/SVG, but don't want the filesize to bloat with thousands of symbols to draw the points?

Learn from my mistakes instead of making your own:

```r
geom_point <- function(...) {
ggrastr::rasterise(ggplot2::geom_point(...), dpi = 300)
}
```
#rstats

I'm reviewing code that I wrote more than 1yr ago for a manuscript. I had a script with ~1000 lines and I just reduced it to 200 by using `purrr::map()` and my custom functions. It's crazy how if you just keep coding you eventually get better. I could go to 100-150 but I need to move on so I'll just leave it as is.

@tedinski @inthehands dealing with an unpredictable support ("sometimes this will unblock a whole thing I didn't know I didn't know but sometimes this is a rabbit hole distracting me") is not a new meta skill of learning strategy. A lot of the folks I know teaching here are adapting the same meta skill building lessons for correcting misconceptions re how we learn. The hopeful side of students dealing with confusing technology imo is that it makes this stuff really immediately relevant to them.

Thanks to a StackOverflow question, I've outlined a method for deploying shiny live apps straight to GitHub Pages from a repository. This approach bypasses storing the converted app within the repo by integrating a GitHub Pages deployment step into the GitHub Action worker, which keeps the repo history focused on only the shiny app source.

Check it out:

👉 https://github.com/coatless-tutorials/convert-shiny-app-r-shinylive

#rstats #shiny #rshinylive

Several of us overly online biologists spent years quietly doing an experiment on Twitter, trying to find out if tweeting about new studies from a set of mid-range journals caused an increase in later citations, compared to set of untweeted control articles.

Turns out we had no noticeable effect; the tweeted papers were cited at the same rate as the control set.

Our paper, headed by Trevor Branch, was published today in PLOS One:

#SciComm #Twitter #X #Science

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0292201

Preprint describing Nellie, a napari plugin for automated organelle segmentation. Results look impressive!

https://arxiv.org/abs/2403.13214

repo (with video): https://github.com/aelefebv/nellie

#CellBiology #microscopy #napari

@neuralreckoning Do they mean it doesn't cover ALL the costs of research but only part of it? In that case, if costs are fairly constant the more overheads they charge the larger proportion of the costs is covered. That's the benign interpretation. I have the impression it's more because of rankings, prestige and such, which in turn brings more funds. It's all business. The more I learn about the more I find evidence modern academia is managed as big corporations.

I am honestly floored at the #SegmentAnything implementation for #ImageJ / #Fiji

Even running on a laptop, once loaded, it's incredibly quick.

Moreover, it's a super-simple install which is a major barrier to many #AI #DeepLearning implementations.

Time to play around with some #Microscopy and #DigitalPathology data!

Details here: https://github.com/segment-anything-models-java/SAMJ-IJ
Photo source: https://www.pexels.com/photo/photo-of-railway-on-mountain-near-houses-1658967/