#Statistics thought of the day: At the heart of much nonsense research lies data analysis (including machine learning) of a complexity that the effective sample size cannot support: hbiostat.org/hdata #StatsSky

I'm greatly appreciating this series of videos about biological modelling with Karthik Raman. I started with the flux-balance models, but now I'm going back to the beginning. www.youtube.com/playlist?lis...

Computational Systems Biology | IIT Madras - YouTube

"This lecture series, part of the ""Computational Systems Biology"" course, focuses on the mathematical modeling of biological systems. It introduces various...

youtube.com

Thanks to input from @helucro.bsky.social, Daria Lazic, Hugo Gruson, Artür Manukyan and many others, there is now a whole new level of maturity and ease-of-use for spatial omics data, see helenalc.github.io/SpatialData....

Wolfgang Huber@wkhuber.bsky.social · 2mo ago

@helucro.bsky.social at CSAMA 2026 csama2026.bioconductor.eu

"The cow is homeostatic for blood-temperature ... If, however, a sensitive temperature-recorder be inserted in the brain and then a stream of ice-cold air driven past the animal the temperature rises without any preliminary fall." The cow must have a model. pespmc1.vub.ac.be/books/Conant...

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...

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

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 🖖

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 😃

a man pointing to a sign that says believe

ALT: a man pointing to a sign that says believe

media.tenor.com

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

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

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...

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 ...

elsevierhealth.com.au

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

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...

📢 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

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

seek.com.au

I continue to be astounded at the number of compositional data analysis packages that will happily report differential abundance of individual species. Did they not understand the concept of compositional data? How is it possible to publish methods with this premise?

Normalization and log transformation of log count data. Pseudocounts, library size adjustment, Centered Log Ratios (CLR), Variance Stabilizing Transformation, and all that. Many variations on a similar task. Here's something I haven't seen done:

Random 2d Turing Machines make interesting patterns. pointersgonewild.com/2012/12/31/t...

Turing Drawings

Turing Drawings

pointersgonewild.com

An experimental design I've seen this three times in different contexts in the last couple of years. The RNA-Seq DE analysis turns out to be non-obvious: You apply treatment X to one group of subjects and treatment Y to another group. You have samples from before and after the treatment.

🧵 PCA is everywhere in bioinformatics—but did you know it’s just SVD in disguise? 1/ If you've done bioinformatics, you've likely used PCA. But did you know Singular Value Decomposition (SVD) is at its core? Let’s break it down. 👇

Happy little accidents...

I'm really liking this course on generative diffusion models. They seem to have boiled many years of confusing development of ideas down to a simple approach. diffusion.csail.mit.edu

Monash University is considering the use of AI assisted assessment. Implementation planned to begin in semester 2 of this year. www.monash.edu/learning-tea...

Comparison of optimization and sampling from a distribution defined by an energy function. I use a continuous version of the Ising model spin lattice energy. First, optimization from a random initial state using gradient descent with momentum, using the SGD optimizer in PyTorch.