Bioinformatician/Genomics Software Engineer @GarvanInstitute, Views my own. Mastodon @Psy_Fer_@genomic.social, https://nitter.cf/t.co/K5efuEeBwt BS: https://nitter.cf/t.co/2xF86mQ9Ug
Sydney, New South Wales
Joined August 2016
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Great way to start the new year, with our platform specific file format for @nanopore signal data, SLOW5.
Better compression, faster analysis, easy to use and read, slow5tools for conversion to and from fast5, and a rich API for devs.
nature.com/articles/s41587-0…
James Ferguson retweeted
Very proud to share the bulk work from my postdoc, now out in @Nature!!
Introducing phase 1 of the TenK10K dataset, with matched WGS and single-cell RNA-seq from almost 2,000 individuals nature.com/articles/s41586-0… 🧬🧵👇 (1/n)
James Ferguson retweeted
My thought on AI review: lh3.github.io/2026/10/27/let…
TL;DR: journals are banning fully AI-generated review and I think that is the right decision
James Ferguson retweeted
Our next Long-Read Research Symposium is less than a month away! Come hear about all the exciting things you can do with @PacBio and @nanopore data. It is FREE to attend - morning tea and lunch included.
Register here - eventbrite.com.au/e/garvan-l…
kuva v0.6.0 is out!
New:
Genome browser layout: stacked tracks on one shared axis, so coverage, variants, amplicons and genes line up column-for-column.
-Typeset math in labels (typst)
-NA handling on the CLI
-15 new colour palettes.
Full release notes:
github.com/Psy-Fer/kuva/rele…
pod5lib-rs v0.2.0 has been released
This release is compatible with pod5 v0.3.49
It is also ~2x faster at both reading and writing pod5 files, and uses less memory (though details are complicated, mmap vs standard io, see docs)
github.com/Psy-Fer/pod5lib-r…
James Ferguson retweeted
Applications for our Summer Scholarships Program are open.
We welcome applications from students who demonstrate initiative, original thinking and a genuine passion for discovery.
🔗Learn more or apply here: ow.ly/JjpF50ZPYhT
#SummerScholarships #MedicalResearch
Sign up for the @GarvanInstitute Long-Read Research Symposium 2026, a day filled with talks/discussions on the latest advances in long-read sequencing technology and related genomics, transcriptomics and epigenetics research using @nanopore and @PacBio
eventbrite.com.au/e/garvan-l…
We are inviting early-career researchers to submit abstracts for limited speaker slots, presenting work alongside our invited speakers. This is an opportunity to share your long-read sequencing research with the community and gain speaking experience at a focused symposium.
Selected speakers will be in the running for a prize of a 50% discount on one genomic library prep and one flow cell*
Apply here:
docs.google.com/forms/d/e/1F…
(*conditions apply, see form)
James Ferguson retweeted
Don't miss the 2026 Garvan Long-read Research Symposium. All the latest updates and discoveries in genomics, transcriptomics & epigenomics, powered by @nanopore and @PacBio technologies. Places are limited places & going fast! eventbrite.com.au/e/garvan-l…
kuva v0.5.0 release!
- CLI plots that print their own Rust code (--emit-code)
- Multi-page PDF export
- Fresh docs site
- A 64th plot type: Pareto chart
- twin-Y axes, date/time X axes, header control (--header), label backgrounds, subtitles
- Security
github.com/Psy-Fer/kuva
James Ferguson retweeted
15 years without an answer. One assay could change that.
Discover how Andre Reis' research is exploring a single, comprehensive approach to investigate the mechanisms of inherited disease and population genomics.
Find out more: nanoporetech.com/resource-ce…
Research use only.
James Ferguson retweeted
A scientific plotting library in Rust. 60 plot types, SVG output, optional PNG/PDF backends, and a CLI binary that renders plots directly from the shell — including in the terminal itself. github.com/Psy-Fer/kuva
I was recently invited to provide a case study along with other researchers for this blog post+pre-print.
My main points are: AI agents are useful, but steering through expertise, verification, responsibility, and support are more important than ever
openai.com/index/scientific-…
The case study covers rustar-aligner (a re-write of STAR into rust), svb (a streamvbyte+VBZ/EX-ZD codec for signal compression), and kuva (scientific plotting library in rust
github.com/scverse/rustar-al…
github.com/Psy-Fer/svb
github.com/Psy-Fer/kuva
James Ferguson retweeted
It was fun being invited to contribute a case study to this @OpenAI preprint + blog 😊
I think it ended up a really nice overview, an interesting cross-section of how multiple people are approaching similar problems...💡
Coding agents are helping scientists spend more time advancing research, taking on everything from routine maintenance and targeted optimization to complete redesigns and new systems.
While agents can reliably execute on ambitious projects, researchers must still define the scientific questions, verify results, and take a stance on long-term ownership.
James Ferguson retweeted
Glad to see this out: in work done w/ @andrewho03, we collected case studies from scientists that have been using agents to accelerate the pace of their work across a range of lifesci applications and discuss some recurring trends
nitter.cf/OpenAI/status/20821520…
Coding agents are helping scientists spend more time advancing research, taking on everything from routine maintenance and targeted optimization to complete redesigns and new systems.
While agents can reliably execute on ambitious projects, researchers must still define the scientific questions, verify results, and take a stance on long-term ownership.
James Ferguson retweeted
Coding agents are helping scientists spend more time advancing research, taking on everything from routine maintenance and targeted optimization to complete redesigns and new systems.
While agents can reliably execute on ambitious projects, researchers must still define the scientific questions, verify results, and take a stance on long-term ownership.
James Ferguson retweeted
Your ancestral background shouldn't limit a genetic test's accuracy. Thanks to a @NSWHealth grant, A/Prof Jodie Ingles' team is expanding our Elusive Hearts Study, working with diverse families to find missing genetic causes of inherited heart conditions.
ow.ly/pygJ50Zt2a8
James Ferguson retweeted
Our bodies replace our skeletons every 10 years. A new global study co-led by Garvan and @MaterResearch has mapped the genes and cells that control this process, laying the groundwork for future therapies to actually rebuild lost bone.
🔗Read more: ow.ly/UTV350ZmLbO
