iiinova — where your digital self keeps evolving

James Ferguson @psy-fer.bsky.social · 02/10/2026

github repo, zenodo, and socials posts about it?

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James Ferguson @psy-fer.bsky.social · 02/10/2026

Though of course, I also have pretty much zero size. So there is that same issue.

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James Ferguson @psy-fer.bsky.social · 02/10/2026

I created r/bioinformaticsdev to be able to talk about tools and development in bioinformatics because of this rule in r/bioinformatics. So if people want to post there, feel free. Obviously I don't want low effort posts, but I think we can all generally agree what that looks like.

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James Ferguson @psy-fer.bsky.social · 30/09/2026

Yea true. I was saying from a molecular bio/bioinformatics/medical research point of view given that's my experience. Either way, it's still insane 😅

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Reposted by James Ferguson

Garvan Institute @garvaninstitute.bsky.social · 29/09/2026

A world-first test developed by Garvan researchers has identified the genetic cause of inherited muscle disease in people who spent years – sometimes decades – without answers. 👉 ow.ly/kvZi50ZStIE #GeneticResearch #InheritedMuscleDisease #DNATest #MuscleDisease #MedicalResearch

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James Ferguson @psy-fer.bsky.social · 29/09/2026

That's insane. That's the equivalent of a few post doc outputs a year in serious labs. The only way to achieve that is to lower the quality and robustness of the science.

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Reposted by James Ferguson

Garvan Institute @garvaninstitute.bsky.social · 22/09/2026

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/PCur50ZPYkf #SummerScholarships #MedicalResearch #CareerDevelopment

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James Ferguson @psy-fer.bsky.social · 22/09/2026

Ooph. There are some things you don't use genAI for. Writing and reviewing is one of them

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James Ferguson @psy-fer.bsky.social · 18/09/2026

If we are going to do this whole AI agent thing, then the next big operating system and app features needs to be "Agent accounts" that can be permission scoped appropriately for better security, rather than acting through our own accounts on everything.

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James Ferguson @psy-fer.bsky.social · 11/09/2026

Back in 2018 we were trying to bully canu into doing better transcript assembly for our nanopore single cell work (yes, we were one of the first 😅 it kinda worked, but it was a mess, and before I had the skills to write a new assembler. So this is kind of exciting 😁

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James Ferguson @psy-fer.bsky.social · 08/09/2026

I still don't like it in creative works. But for stem (and done right) I'm okay with it. I think many people generally need to put the chatbots down though, especially boomers 😁

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Reposted by James Ferguson

Jovana Maksimovic @jovmaksimovic.bsky.social · 31/08/2026

Gene fusions drive ~16% of all cancers & 50-70% of childhood ALL. But standard scRNA-seq can't see them — the assays aren't built to capture fusion breakpoints. We built a way to fix that. @aliciao.bsky.social @sadras-t.bsky.social @petermaccc.bsky.social @onjcri.org.au @10xgenomics.bsky.social 🧵

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James Ferguson @psy-fer.bsky.social · 04/09/2026

Same! that linear regression plot sent me into a full belly laugh. I just don't understand people like this. So weird.

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James Ferguson @psy-fer.bsky.social · 04/09/2026

On Insta he keeps saying things like because it's MIT and open source, that he can do whatever he wants... meanwhile, the MIT has ONE requirement, and he absolutely has to honour it in this case. Like, you can't just make shit up.

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James Ferguson @psy-fer.bsky.social · 02/09/2026

I keep seeing stuff like this. Saw something today on LinkedIn about signal based analysis and how it was a breakthrough. Like mate, I was doing signal based readuntil and real time signal based alignment like 10 years ago. These days we have signal based alignment that gives paf output 😅

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James Ferguson @psy-fer.bsky.social · 31/08/2026

This was one of the coolest sup figures I made in one paper, showing how poor signal segmentation in ONT minknow software can lead to double barcodes or other signal abnormalities impacting accuracy of methods.

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James Ferguson @psy-fer.bsky.social · 31/08/2026

I am much newer to publishing (2019 being my first paper). Sups to me seem like an absolute must, and it's where I can also shove some of the weird exceptions and side experiments, and background benchmarks that don't fit in the paper, but are what shaped the choices that made it (but can't cite)

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James Ferguson @psy-fer.bsky.social · 31/08/2026

Not everyone is a good actor in terms of collaborating in science. And so you could ask for the details not provided and they ignore you or tell you to shove it. only for them to bring up that data in a review later (You may guess why this is so specific 😅 ). Open Science is always better.

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James Ferguson @psy-fer.bsky.social · 31/08/2026

Yea but that's how we got into the mess of "code available upon reasonable request" and large tables in PDFs, and all other kinds of silliness that should have been an easy solve with the internet. Not arguing for a structural change, just saying sups are important for completeness.

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James Ferguson @psy-fer.bsky.social · 31/08/2026

You kind of missed the point I was making. Also, I disagree. Conclusions without the details are good for headlines not science.

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James Ferguson @psy-fer.bsky.social · 30/08/2026

But also, there are many ways to read a paper depending on the purpose. People building on the work read the Sups. People referencing the material for its contribution or conclusions don't.

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James Ferguson @psy-fer.bsky.social · 30/08/2026

My problem is journals still pushing "print" limitations on online only publishing and charging me for it. Having to put things in the Sups because it doesn't fit in their limits. I always found the most interesting things in the Sups as they always contained the cool technical stuff.

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James Ferguson @psy-fer.bsky.social · 29/08/2026

Haha yea I've been thinking about this for something else because the disease phenotypes are complicated. Probably made simpler if we logged the protein structures in populations

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James Ferguson @psy-fer.bsky.social · 28/08/2026

They made more than probably both our salaries combined 😅

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James Ferguson @psy-fer.bsky.social · 28/08/2026

I heard stories about people working at GAFAM that would build all different kinds of things that would never get released. Changes that happened only so change was seen, but not for any actual improvement to a product. Sometimes as small as just changing a colour slightly or the shape of a button.

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James Ferguson @psy-fer.bsky.social · 28/08/2026

Man, I was just saying the same thing yesterday 😅

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James Ferguson @psy-fer.bsky.social · 28/08/2026

Maybe someone should fix that

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James Ferguson @psy-fer.bsky.social · 28/08/2026

Software overall has gotten worse the last few years. Simple things like the video player on Netflix or a simple messaging app or word processor or code editor, are all becoming flaming piles of crap with each update.

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James Ferguson @psy-fer.bsky.social · 27/08/2026

Absolutely. The paper is finished with the pre-print. It's refined in the reviews, and wrapped up on publication. Usually by then i'm working on something else or the next step, so less of a big deal.

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James Ferguson @psy-fer.bsky.social · 27/08/2026

I published my first paper in 2019. It had a preprint first, as has every other paper I've published since (and at least 90% of all I'm a co-author on too). Don't really understand why someone wouldn't preprint.

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James Ferguson @psy-fer.bsky.social · 27/08/2026

I mean, at least it's the right direction, compared to the one you originally commented on 😅

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James Ferguson @psy-fer.bsky.social · 27/08/2026

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.

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James Ferguson @psy-fer.bsky.social · 27/08/2026

Sign up for the Garvan 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 @nanoporetech.com and @pacbio.bsky.social www.eventbrite.com.au/e/garvan-lon...

eventbrite.com.au

Garvan Long-Read Research Symposium 2026

Join us at the Garvan Long-Read Research Symposium 2026 for a deep dive into groundbreaking discoveries in medical research!

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James Ferguson @psy-fer.bsky.social · 24/08/2026

If I encountered this Kitten, and they didn't have a forever home, they would from that point on. My other black fluffies would be happy for another friend

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James Ferguson @psy-fer.bsky.social · 24/08/2026

99% sure I know who you are talking about, and while I was studying physics, I thought his ideas on how the brain worked were pretty insane. Then I moved into biology and was only more sure of it than before 😅

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James Ferguson @psy-fer.bsky.social · 21/08/2026

Yea even just a cool down in general would help with many supply chain attacks due to them usually being detected within a few weeks.

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James Ferguson @psy-fer.bsky.social · 20/08/2026

Ahh yes, the dog genome I built will do splendidly at your nanomaterials conference.... Also, any claim of impact factor (usually around 4ish) is a red flag 😅 I wish I knew why these spam emails latch on to one paper and just keep going for years on end.

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James Ferguson @psy-fer.bsky.social · 20/08/2026

Do you ever get an email, but you see it mentions that one paper from a few years ago, and just instantly know it's spam? For me it's "Chromosome-length genome assembly and structural variations of the primal Basenji dog Canis lupus". I don't think i've had a legit email about it since it came out

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James Ferguson @psy-fer.bsky.social · 20/08/2026

Ahh, so I'm not the only one who read that and went "well I guess that phase of enabling science is over, shareholders gotta eat!"

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James Ferguson @psy-fer.bsky.social · 19/08/2026

I really hope pac bio can find its way through. The data is pretty great, and after some solid investment around on long read cohorts we are starting to see the benefits.

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James Ferguson @psy-fer.bsky.social · 15/08/2026

Fun hobby stuff, like your pore tetris game, would fit well

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James Ferguson @psy-fer.bsky.social · 15/08/2026

As a bioinformatician, what will I want to read/post/comment there?

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James Ferguson @psy-fer.bsky.social · 12/08/2026

I got pulled up in a review because one of my functions had a swear word in it, and some of my comments had me basically arguing with myself over how to do something. Like, what? Now I'm watching LLMs basically do the same thing (without the bad words)

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James Ferguson @psy-fer.bsky.social · 12/08/2026

Half my stuff is a mix of British and US English. Mostly because I'm Australian and I spell British but code US. So things get weird 😅

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Reposted by James Ferguson

Rob Patro @robp.bsky.social · 10/08/2026

2.3 billion read pairs of 10x Flex v2 (281 GB of gzipped FASTQ) mapped in under 2 minutes on one machine (-t 64) with piscem-rs. That's ~20M read pairs/sec at ~87% mapped. One interesting part is the mapper, but what I want to talk about here is who gets the threads. 1/8

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James Ferguson @psy-fer.bsky.social · 11/08/2026

So back when the pandemic hit, we were doing the sequencing for contact tracing, and needed a quick way to asses coverage across the amplicon pools. So I made CoVarPlots to do that (img1). I've now ported that across to kuva with some more functionality (img2). Coming in v0.6

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James Ferguson @psy-fer.bsky.social · 09/08/2026

I wish I could get paid to sit in a meeting with government people and be like "here are 20 ways I could do big bad and how to do it... Do something about that" and call it consulting or something. But they write everything down and I just get money and don't have to quit my day job.

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