James Ferguson

Postdoc Description.docx Title: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...

Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...

And let’s be clear, funding discovery research is not charity, it's not just about keeping weirdos like me off the streets, IT PAYS FOR ITSELF

AAMRI/KPMG found that every $1 invested in Australian medical research returns $3.90 to the economy

👏Translation 👏dries up 👏if you stop feeding 👏the pipeline 👏of discovery👏

#NHMRCdraftStratergy #Ihavenotes #ValueFundamentalScience

Dear Everyone, I've read the #NHMRC draft strategy and I have notes ...

So I'm going to...🧵🤔🧵😱🧵😵‍💫🧵🙏🧵🧵🧵
This is a repost from X because you all need to know!

#NHMRCdraftStratergy #Ihavenotes #ValueFundamentalScience

@nhmrc.bsky.social

Adaptive sampling #WGS is moving from bench to bedside. Our work delivers SNV, structural & methylation insights on @nanoporetech.com with molecular signals emerging in minutes, not days. Watch this space 👀 #cancer #genomicAI #MultiOmics #bioinformatics @cra-chusj.bsky.social
tinyurl.com/4d337djb

Like, why not cite their papers AND the originals? It's not like we limit references 😅

Your masters student knows what's up 😎

A more pretty one from a while back

only the first time ;)
Once you have a good template set up, things are super easy. My stuff is mostly screenshots and diagrams with basic text anyway, explaining algorithms, pipelines, data structures, or pretty annotated squiggles/sequences

(here is a not so pretty example)

And, you can still do pretty things with it

I guess it's over for me 😅

I like it for it's simplicity. I don't like all the AI crap in PPT now. I also mainline linux, and so having browser based slide maker is just easier for jumping between systems. Online PPT vs installed is...weird. LibreOffice does okay, but again, G-slides is just easier

Well shit...everything I do is in google slides

A complete diploid human genome benchmark for personalized genomics Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

I had neighbours that had their fire alarms going off during the day while they were at work. They had no idea. Then they didn't believe me. I played them a video, and they said "that isn't coming from our house". That very night, at 2am, it went off again. Couldn't stop laughing 😅

Adaptively integrated sequencing and assembly of near-complete genomes Recent advances in long-read sequencing (LRS) and assembly algorithms have made it possible to create highly complete genome assemblies for humans, animals, plants and other eukaryotes. However, there...

Hey, Yea our group has had some great success with hifiasm. It has an ONT option now too. We have been building human genomes with ONT and PB data. We also made a new method:
www.biorxiv.org/content/10.1...

Flye is also pretty great. Polishing has a few options and best opton changes often

Oh wow, that's so cool

what!?!?!

I am now hungry. Thanks for that

😆

I can't seem to get a simple answer to a github issue, so probably not.

Congratulations to @hasindu2008.bsky.social form #UNSW Computer Science and Engineering for wearing a tuxedo last night 👏🏻
Also for being awarded the #EurekaPrize for outstanding early career researcher, showcase his pioneering and impacftful research in #bioinformatics software

I run windows 11 and a few different linux distros on various computers. Never had an issue with any of them. I don't get it

#A-RNA2025 off to a great start. @martinalexsmith.bsky.social sharing his views on why lncRNAs should no longer be consider wallflowers.

Just found I needed a new bit of data in an output of a tool in Rust. It involves adding to the main struct, and propagating that through all the complicated bits in the software all the way to the output writing stage.
It was pretty easy to refactor, with compiler/rust analyser. Love this language

I built and installed this absolute beast of a machine for
@nanoporetech.com
basecalling
@petermaccc.bsky.social

Threadripper
4x5090, liquid cooled
128gb DDR5 ram
~40Tb of nvme and SSD storage
TWO power supplies, a 1200W and a 2500W
All in a Corsair 9000D case

~5^7 samples/second with dorado.

Oh, how loud are they? I wonder what kind of furniture this could be place in, to make like, seamlessly integrated filteration in every room.

Yea fair enough. I'm a control freak for mess when i make stuff. But then i'm also very slow because of it.

How much of that max CFM do you think you actually get out of that?
Also that board would drive me nuts with all the mess 😅

Join us for a day (Nov 13) of fascinating talks and discussions on the latest in long-read sequencing tech and related research in genomics, transcriptomics, and epigenetics. A great opportunity to network and hear from leading experts from around Aus.

www.eventbrite.com.au/e/garvan-lon...

GitHub - Kirk3gaard/2025-Crowdsource-GPU-basecalling-stats: A repository for collecting GPU basecalling stats A repository for collecting GPU basecalling stats. Contribute to Kirk3gaard/2025-Crowdsource-GPU-basecalling-stats development by creating an account on GitHub.

This is of course tested with the dataset from @kirk3gaard.bsky.social and comparing to the benchmarking repo

github.com/Kirk3gaard/2...