Ira Cooke

We ran a randomized controlled trial to see how much AI coding tools speed up experienced open-source developers.

The results surprised us: Developers thought they were 20% faster with AI tools, but they were actually 19% slower when they had access to AI than when they didn't.

DNA metabarcoding provides new insight into the diet of invasive chital deer (Axis axis) in a tropical savanna landscape The introduction of non-native species into new environments can cause significant ecological harm and is considered a major conservation threat. As populations of invasive species continue to establ....

Ever wondered how DNA metabarcoding compares to traditional methods for assessing diet? Curious whether these techniques could help inform the management of introduced deer in Australia? Then our latest research is for you!

@janstrugnell.bsky.social @coatiben.bsky.social

doi.org/10.1002/ecs2...

@zoologistedel.bsky.social wowing the crowd about her genomic research on Heard and McDonald Islands #pintofscience

Joe Perkins entertaining the audience in his precompletion PhD seminar on Ecology, detection, and impacts of benthic toxic dinoflagellates in Qld: a focus on #ciguatera poisoning. @marine-omics.bsky.social 🧬

New blog post!
In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup.
Check it out for the full results:
rrwick.github.io/2025/05/27/d...

Is there a core response to heat stress in #abalone? You bet there is. Check out this fantastic new meta-analysis of heat stress studies across abalone led by Roy Barkan. @marine-omics.bsky.social @iracooke.bsky.social 🧬🧬 rdcu.be/elVL2

Putting Structural Variants Into Practice: The Role of Chromosomal Inversions in the Management of Marine Environments Major threats to marine species and ecosystems include overfishing, invasive species, pollution and climate change. The changing climate not only imposes direct threats through the impacts of severe ....

Putting Structural Variants Into Practice: The Role of Chromosomal Inversions in the Management of Marine Environments. New @marine-omics.bsky.social paper by Nadja Schneller with @janstrugnell.bsky.social, @mattfield100.bsky.social and Kerstin Johannesson out today doi.org/10.1111/mec....

YouTube video by SAEF - Securing Antarctica's Environmental Future Our seafloor history teachers

Big thanks to the fabulous crew, deck officers and all the expeditioners onboard RSV #Nuyina on our voyage to the Denman Glacier, East #Antarctica. @arcsaef.bsky.social @jcuofficial.bsky.social @marine-omics.bsky.social @lausally.bsky.social 🐙🇦🇶🧬 www.youtube.com/watch?v=KAhD...

Postdoctoral Research Fellow, Population Genomics - Townsville, QLD, Australia James Cook University (JCU) is creating a brighter future for life in the Tropics and beyond, through education and research that makes a difference locally and globally.  We now have an opportunity a...

We @marine-omics.bsky.social are hiring. We're looking for a postdoc in population genomics. @janstrugnell.bsky.social careers.jcu.edu.au/jobs/postdoc...

Hands raising a toast with test tubes.

A crowd at the Lincoln Memorial in DC with signs, including “Defend Science like lives depend on it. (They do)”

Raise a test tube for the brilliant, courageous young scientists who organized today’s #standupforscience rallies.
You are my heroes. Well done! @standupforscience.bsky.social 🧪

Wild frontiers of model organisms

Still time to submit an Abstract for the @embl.org symposium on the Wild Frontiers of Model Systems !
If you’re into unconventional, non model systems, bringing more ecology in our understanding of biological processes, Lab-field interface this is for you.
www.embl.org/about/info/c...
#protistsonsky

GitHub - symgenoevolab/SyntenyFinder: SyntenyFinder contains a collection of scripts to easily perform and visualize macrosynteny analysis when provided with the accessions of annotated chromosome-lev... SyntenyFinder contains a collection of scripts to easily perform and visualize macrosynteny analysis when provided with the accessions of annotated chromosome-level genome assemblies from NCBI. - s...

To support genome structure studies in non-model systems, we developed SyntenyFinder, a synteny analysis pipeline combining OrthoFinder and RIdeogram. Learn more on our GitHub: github.com/symgenoevola...

Some years ago I wrote a simple R app to explore colors in HCL space. While it's clunky, it still is my preferred way of selecting colors, because it offers features other color selectors don't normally have. Today, thanks to shinylive, the app is available standalone. 🧵

A great year for Marine Omics! www.marine-omics.net

🤯 "perhaps most great whales have an unrecognized potential for great longevity that has been masked by the demographic disruptions of industrial whaling. This unrecognized longevity has profound implication for basic biology and conservation of whales." Astonishing stuff.

🚨New Preprint🚨: A Single-cell Atlas of Coral Bleaching! 🪸🦠🔥. We show the microbial ecology of coral bleaching from the gene expression of host and symbiont cells to the shifts in the bacterial and protist communities within the holobiont! #ProtistsOnSky #SymbioSky #MicroSky 🧪

Lot's of neat tricks here 👏

credit: Liam Lachs

📢New Paper Alert📢

on corals and climate change in Science

Adaptation via natural selection could determine whether Acropora corals persist under expected levels of global warming

Hyperlinks & explainer thread below ⬇️

(1/12)

Divergent reference genomes compromise the reconstruction of demographic histories, selection scans, and population genetic summary statistics https://www.biorxiv.org/content/10.1101/2024.11.26.625554v1 Characterizing genetic variation in natural populations is central to evolutionary biology. However,

Divergent reference genomes compromise the reconstruction of demographic histories, selection scans, and population genetic summary statistics https://www.biorxiv.org/content/10.1101/2024.11.26.625554v1

New publication from the amazing Joe Perkins explores #dinoflagellate abundance & diversity in Hervey Bay, Qld using #DNAmetabarcoding. First-time identification of some #toxin-producing species in Australia!🧬

www.sciencedirect.com/science/arti...

I just ran my 1.5 hour HTML+SVG+JavaScript+D3 workshop at ResBaz Victoria 2024. Touched on hopefully most of the important ideas needed for an interactive web-based data visualization. #resbaz #resbazvic #resbazvic2024

pfh.github.io/jsfoot/

Pangenome construction from short-read sequences: benchmarking for population and conservation genomics As a collection of all the genetic variants in the gene pool, the pangenome is a concept that will become fundamental to conservation genomic studies. Unfortunately, most pangenomic approaches develop...

Very timely!!
#Pangenome construction from short-read sequences: benchmarking for population and conservation genomics

www.authorea.com/users/616600...

Misinformation Laws Not Necessary, Says Meth Addict Peter Dutton — The Shovel Speaking from a prison cell in Brisbane, Mr Dutton – a former sex worker and director of adult films – said the laws were not necessary and that regulators should not be the arbiters of truth.

Misinformation Laws Not Necessary, Says Meth Addict Peter Dutton

looks like it’s time for altimetric to skip twitter and include Bluesky or maybe even better just add Bluesky - would be nice to see where more science dissemination occurs!

Hi Mel I am not sure to be honest. I had mine mostly complete. We will find out tomorrow now I hope

Action Intent Links | Bluesky Authors, websites, and apps can use action intent links to implement "Share on Bluesky" buttons, or similar in-app actions. Logged-in users will be directed to the corresponding action view in the Blu...

We strongly suggest that academic publishers and other platforms that host research rapidly implement a Share to Bluesky button for their articles. Here's how:

docs.bsky.app/docs/advance...

#AcademicSky #HigherEd #Altmetrics

It’s a free text field so that’s what I plan to do. Probably not a real issue but just highlights how ridiculous the situation is

Prepping an EOI for DP 2025 without knowing the 2024 outcome. RMS is warning me that I will be over the grant limit if I am successful and asks me to nominate a grant that I would withdraw from. I don't want 3 grants. I just want to reapply for the one I might not get. @arc-tracker.bsky.social

Many coral 'species' may, in fact, be separate 'cryptic' species! We found that up to 68% of #popgen studies in corals had putative cryptic taxa!! Check out the ms in Peer Community Journal! @peercommunityin.bsky.social
#corals #crypticspecies

peercommunityjournal.org/articles/10....

Top work Nikki Rodewald taking hope the best poster prize at the Australian Antarctic Research Conference #AARC2024 for her PhD research on #Labidiaster ⭐🧬🇦🇶