Zamin Iqbal
@zaminiqbal.bsky.social
6K followers 4.7K following 880 posts
Professor of Algorithmic and Microbial Genomics at the University of Bath (UK). Pangenomes, drug resistance (esp TB), data structures for DNA search, plasmid evolution, global microbial surveillance. Open Data, reproducibility
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zaminiqbal.bsky.social
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Reposted by Zamin Iqbal
Reposted by Zamin Iqbal
profannawatts.bsky.social
Lol the Nobels can't even acknowledge women's contribution to discovery. But sure let's acknowledge The Machines.
Headline from an article in Nature this week that states "Prizes must recognize machine contributions to discovery. The future of science will be written by humans and machines together. Awards should reflect that reality."
zaminiqbal.bsky.social
This is wonderful to play with, highly recommended for anyone who wants to understand the BWT
robert.bio
Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt

It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
Reposted by Zamin Iqbal
peaseroland.bsky.social
Science in Action, coming up, in which I get to revisit, thanks to this week's #NobelPrize, my enthusiasm for 3D organic framework structures, with archive of Omar Yaghi and commentary from @philipcball.bsky.social

And share with listeners that the prog dies in 3 weeks
www.bbc.co.uk/programmes/w...
www.bbc.co.uk
Reposted by Zamin Iqbal
carlzimmer.com
Today my @nytimes.com colleagues and I are launching a new series called Lost Science. We interview US scientists who can no longer discover something new about our world, thanks to this year‘s cuts. Here is my first interview with a scientist who studied bees and fires. Gift link: nyti.ms/3IWXbiE
nyti.ms
zaminiqbal.bsky.social
result <- c(result, current)
result

I think this works, and avoids regex. Regex is fine if you use it frequently, but I don't these days and find it hard to read
(full disclosure, I got chatgtp to offer me solutions and kept rejecting til i saw this)
zaminiqbal.bsky.social
x <- "A,B,C, D"
chars <- strsplit(x, "")[[1]]
result <- c()
current <- ""
for (i in seq_along(chars)) {
if (chars[i] == "," && (i == length(chars) || chars[i + 1] != " ")) {
result <- c(result, current)
current <- ""
} else {
current <- paste0(current, chars[i])
}
}

contd on reply
zaminiqbal.bsky.social
Thanks Ben - they look great!
Reposted by Zamin Iqbal
adamjkucharski.bsky.social
In discussions of AI for epidemic modelling, important to remember that a simple SIR model is the equivalent of print("Hello World") – a useful introductory step, but only the very start of the work required for a good model.
zaminiqbal.bsky.social
Obviously, I can and will sit down and ramble/explain, but wondering about other sources
zaminiqbal.bsky.social
Does anyone know good intro videos describing "big picture" what sequence-analysis (ie mapping, assembly) is all about? I'm going to dig through @benlangmead.bsky.social 's amazing trove of videos, but I think they may be too compsci oriented for the biology student who's asking me about it
Reposted by Zamin Iqbal
simonwillison.net
I figured out a uv recipe for running tests for any project with pyproject.toml or setuppy using any Python version:

uv run --python 3.14 --isolated --with-editable '.[test]' pytest

I've wrapped it in a uv-test script:

uv-test -p 3.11

Full details here: til.simonwillison.net/python/uv-te...
setup.py
Reposted by Zamin Iqbal
iandunt.bsky.social
Trump's $100,000 skilled worker visa fee gives Britain a golden opportunity to attracted global talent. Needless to say, we're going to piss it away because we're scared of upsetting Nigel Farage.

inews.co.uk/opinion/trum...
Trump's migrant obsession offers Starmer a rare win - but Farage has scared him off
We have a golden opportunity to kick-start the British economy
inews.co.uk
Reposted by Zamin Iqbal
josephcox.bsky.social
New: Apple banned an app that simply archived videos of ICE abuses. Rather than other apps that record ICE official's real-time location, Eyes Up is to "preserve evidence until it can be used in court." Videos from TikTok etc. Every submission manually reviewed

www.404media.co/apple-banned...
Apple Banned an App That Simply Archived Videos of ICE Abuses
Eyes Up's purpose is to "preserve evidence until it can be used in court." But it has been swept up in Apple's crackdown on ICE-spotting apps.
www.404media.co