It's slightly maddening that cybernetic negative-feedback control loops *in particular* are not observable from correlation.

I've recently been exploring an Ornstein-Uhlenbeck SDE model of scRNA-Seq and Perturb-Seq. It's a simplistic model, but is enough to encounter many concrete problems that come up in stochastic models, such as parameter identifiability.

Some rough slides here.
logarithmic.net/2026/sde/sde...

This is a case where you could do a TREAT test (T-test RElative to A Threshold) to test for a biologically meaningful difference. limma, edgeR, and DESeq2 all support this, for example. Or the FDR has an under-used confidence interval form, the FCR.

A question: How do biologists learn experimental design? Any suggestions for good textbooks or notable people responsible for current practices?

(I recently failed to convince some collaborators doing an experiment about data-visualization of the importance of a positive control.)

For example parquet is a high performance format, but writing was a bottleneck until I wrote to multiple files at once. The arrow library then makes it easy to read across multiple files at once.

Zarr is another format that seems to lean-in to this idea, but I don't have much experience with it.

Minor theme this year: There's a rough right number of files to split datasets into. For my data, on the order of 100s of files.

Too few, can't process in parallel. Want to be writing in parallel now!

Too many, filesystems go slow or break, especially network/cloud storage. HPC team becomes sad.

Shared my talk “Visualise your fitted non-linear reduction model in high-dimensional space” at ASC2025, Curtin University, Perth.

Great conversations, great people, and so much inspiration. ✨

Slides: jayani-asc2025.netlify.app

#ASC2025 #Statistics #DataScience #Visualisation

This is my simplified version which I use to illustrate different types of error bars:

logarithmic.net/2017/dance/

Love this type of thing. I particularly like repeatedly sampling Confidence Intervals as a teaching tool. There's a web app that goes with a book caled "The New Statistics" where they call this the "Dance of the CIs".

esci.thenewstatistics.com

Shiny - Non-blocking operations Shiny is a package that makes it easy to create interactive web apps using R and Python.

I should also note Shiny's own version of this, ExtendedTask, similarly allows an app to remain responsive.

If inputs to an ExtendedTask change while it is running, the new computation is delayed until the current one finishes. This isn't ideal for my application.

shiny.posit.co/r/articles/i...

I'm trying using background workers in Shiny.

Pattern: Cache results on disk. On a cache miss, launch-and-forget a background worker, tell Shiny to invalidate later, and throw an error for Shiny to display. Workers use file locks to avoid doubling up work.

App remains responsive!

#R #Shiny

It's not just because @torstenseemann.bsky.social is a bioinformatics legend but this may be my favourite #abacbs2025 poster because I'm a #trek tragic 🖖

a man pointing to a sign that says believe ALT: a man pointing to a sign that says believe

Congrats @lonsbio.bsky.social on being awarded the inaugural @abacbs.bsky.social Nick Wong Community Building Award at #abacbs2025! @hdashnow.bsky.social was absolutely right - you really are the Ted Lasso of Australian bioinformatics and computational biology 😃

just added the MEGA TERMINAL CHEAT SHEET from "The Secret Rules of the Terminal" to our list of posters at wizardzines.com#posters

The splats can also be used as weights for local model fitting.

Pondering k-Nearest Neighbor density estimation. There's some subtlety making the density smooth and integrate to 1. Here is a simple scheme:

- Assign each point a radius from the distance to its kth nearest neighbor.
- The density is the sum of a set of Gaussian splats with those radii.

"... a fundamental question that often remains overlooked is whether or not model parameters can be confidently estimated from the available data."

Heatmap in ggplot2
yunuuuu.github.io/ggalign/ind...
I always use complexheatmap, but this seems to be a good alternative if you want to stay within the ggplot

*Grimes

If you've ever wondered why medical research has so many Chesterton's Fences, or what it would actually take to "do your own research", this would be a good starting point. (The target audience of the book is doctors seeking to use published medical research.)

Essential Concepts in Clinical Research: 2nd edition | Kenneth Schulz | ISBN: 9780702073946 | Elsevier Australia Bookstore This practical guide speaks to two audiences: those who read and those who conduct research. Clinicians are medical detectives by training. For each patient, they assemble clinical clues to establish ...

Happened to pick up "The Lancet Handbook of Essential Concepts in Clinical Research" (Schulz and Graves). A short read and surprisingly excellent. You can really tell that the authors have seen it all.

www.elsevierhealth.com.au/essential-co...

I did get the AMS. Not quite sure what I'm doing with it. Maybe some interesting possibilities mixing soft and hard materials.

I've heard good things about marble PLA.

A picture of a 3D printed whistle in front of a 3D printer.

uvx demakein

I've finally updated my wind instrument design program to Python 3. It only took me 10 years to get around to. I was pleased to find there is now a fairly solid python library for 3D boolean operations (manifold3d).

github.com/pfh/demakein

with apologies to grugbrain.dev

grug brain bioinformatician not trust maximum a posteriori estimate. big brained bioinformatics shaman develop map estimate. danger! noise demon hide deeper in data! grug prefer count matrix. grug know what to do when have count matrix.

Excited to announce our first interactive article on sandbox.bio, about genomic ranges: sandbox.bio/concepts/gen...

Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!

🚨 Exciting PhD Opportunities with MACSYS! The MACSYS team at Monash University is offering multiple fully funded #PhD scholarships for students eager to explore the cutting edge of computational biology, microbiology, and systems modelling.
👉More info/apply: macsys.org/monash-phd-s...

👩‍💻 We’re hiring! Lê Cao Lab at Uni Melbourne @mig-unimelb.bsky.social needs an R dev to power the next-gen of mixOmics 🚀
Love #RStats, #Bioconductor & multi-omics? Help expand mixOmics, run workshops & publish cutting-edge methods.
Apply: unimelb.wd105.myworkdayjobs.com/en-US/UoM_Ex...

Research Officer - Bioinformatics Job in Fitzroy, Melbourne VIC - SEEK Seeking a Postdoc to develop computational toolkits to enable large-scale studies of single-cell and spatial 'omics and statistical genetics

📢 PostDoc opportunity in our Bioinformatics & Cellular Genomics lab at SVI! 🧬

You’d join a welcoming, supportive, and brilliant team.

Why not spend a few years in Melbourne and be part of something exciting?

Apply here: www.seek.com.au/job/84737876

#ScienceCareers #PostDoc #Bioinformatics

Parquet format and the arrow library have been life changing.

(I suspect I should be getting on board with duckdb one of these days too.)