iiinova — where your digital self keeps evolving

Amanda Warr @amandatron89.bsky.social · 28/09/2026

Just thinking about how totally normal my office is.

Shelf with minion sequencers, nanopore stickers, wooden dinosaur models, a model of a pig riding a Champaign bottle, and a guitar from the Philippines.

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Rob Noble @robjohnnoble.bsky.social · 02/09/2026

Figure 3 makes it plain

Respondents were asked to indicate the degree and direction of the impact of federal and state policies since January 20, 2025 on the categories of "Impact on my field of science", "Impact on my Department and Institution", "Impact on my research", "Impact on my career prospects", and "Impact on my personal life". A percentage of respondents reported positive impacts in each category (~1-2%). 79.7% of respondents said that federal policies since January 20, 2025 had "extremely negative impact" or "irreparable harm" on their field of science (Figure 3, top row), with a total of 96.8% of respondents saying the impacts have been negative. Over half of respondents said the effects on their department/institution were "extremely negative" or "irreparable harm" (54.8%), with a total of 91.9% responding that the impacts have been negative (Figure 3, second row). Most respondents reported "slightly negative" to "extremely negative" effects on their research (78.4%) and career prospects (70.9%), with about 15-22% reporting no impact and 5-6% reporting irreparable harm in both categories (Figure 3, third and forth rows). A majority of respondents reported slightly negative to extremely negative effects on their personal life (82.3%), with 5.3% reporting irreparable harm and 11.1% reporting no impact (Figure 3, fifth row).

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Amanda Warr @amandatron89.bsky.social · 10/08/2026

As if all of the world's scientists, doctors and nurses are paid enough to lie about it all.

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Flo Débarre @flodebarre.eurosky.social · 29/07/2026

New set of documents released by Rand Paul's staff before Fauci's hearing today. They found nothing. Paul and other conspiracy theorists keep talking about a lab leak cover-up, but to have one, you need something to coverup. They have not found any evidence, in spite of all their subpoenas.

paul.senate.gov

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Amanda Warr @amandatron89.bsky.social · 27/07/2026

Oh lord, I just discovered the preprint he put out. I don't think it is the paper that included shellfish, but the other one that had algae and mushrooms. I did try to stop him.

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Amanda Warr @amandatron89.bsky.social · 22/07/2026

I love the game of "where did the notification ding come from?" while working with multiple windows and a remote desktop that also has multiple windows.

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Amanda Warr @amandatron89.bsky.social · 20/07/2026

School is bringing in a literal hostage negotiator to teach conflict resolution to the staff and students. Sounds about right.

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Amanda Warr @amandatron89.bsky.social · 17/07/2026

There might not be enough caffeine in the world to get me through that chunk of text.

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David Eccles 🌻🇵🇸7x🩹🛡️ @gringene.org · 14/07/2026

If only Flongle were still a viable option: * Run reagent consumable cost of $78.50 (Flongle flow cell + Rapid Barcoding kit); that's quite a cheap sequencing run. That gives barcodes for up to 24 samples; less than $5 per bacteriophage.

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Amanda Warr @amandatron89.bsky.social · 13/07/2026

Although that feels like a me problem, I should probably have bioinformatics in my bio 😅

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Albert Vilella, PhD. @albertvilella.bsky.social · 13/07/2026

I am doing more investigating on the uptake of @bsky.app by the #Bioinformatics and #ComputationalBiology community. I found 2114 accounts where the Bio contains the words "Bioinformatics" or "Computational Biology", out of which the large majority are personal but there are some institutional ones.

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 01/07/2026

We’re happy to introduce phageFACTor (Functional Annotation and Curation Tool) 👩‍💻Developed by Tanaïs Moreau, our most recent PhD candidate, and building on Phold, we were able to improve annotation of prophage genes by as much as 50% 🧬 You should check it out github.com/TMs-code/pha...

In this example, we're showing the improvement in the percentage of annotated genes from prophage "Maintenon" from Clostridium innocuum (doi: 10.1186/s40168-023-01541-x) using the phageFACTor pipeline

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 08/06/2026

Is @nanoporetech.com hac v6 better than 5.2.0 sup? The short answer is no. But are a few errors in a genome worth 5 times more basecalling compute? github.com/Kirk3gaard/M...

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Ryan Wick @rrwick.bsky.social · 11/06/2026

New blog post! I analyse the new hac@v6.0.0 basecalling model from @nanoporetech.com and discuss the conspicuous lack of a new sup model: rrwick.github.io/2026/06/11/d...

rrwick.github.io

Dorado v2.0.0: no more sup?

a blog for miscellaneous bioinformatics stuff

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Amanda Warr @amandatron89.bsky.social · 24/06/2026

Anyone have a favourite tool for simulating nanopore reads at current error profile? Still badread?

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Amanda Warr @amandatron89.bsky.social · 19/06/2026

We're going to need a video of the result

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David Eccles 🌻🇵🇸7x🩹🛡️ @gringene.org · 15/06/2026

From the presentations I watched, RNA barcoding does seem to be working fine. Yes, ONT's claim is that the new HAC is better than the old SUP, so there's no need to improve further. I don't agree. There is substantial marketing benefit from catering to the people who want higher accuracy.

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Amanda Warr @amandatron89.bsky.social · 15/06/2026

Also keen to hear about any new(ish) host depletion kit options. I have a lot of (unfortunately very frozen) intestinal samples (fortunately with glycerol) that are (unfortunately) bonkers littered with host cells.

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Amanda Warr @amandatron89.bsky.social · 15/06/2026

Thanks David! I spotted the barcodes, does it seem like the kit works pretty well? Last time I used direct RNA the throughput and accuracy was still pretty weak. Is that SUP going because HAC improved enough? I've still yet to actually get to use my P2 Solo 😩 other people have been using it though

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Amanda Warr @amandatron89.bsky.social · 15/06/2026

I'd heard about Andes, that one was hard to miss, but definitely completely missed RVFV 😅 Not too sad to have missed either of them! New ARTIC stuff and peartree is good to know, thanks!

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Amanda Warr @amandatron89.bsky.social · 15/06/2026

I'm just back at work after an 11 month absence. What did I miss? Nanopore stuff? Virus stuff? Microbiome stuff? Important new tools? Fill me in.

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Amanda Warr @amandatron89.bsky.social · 08/04/2026

Has anyone ever been awarded the Nobel Peace Prize after threatening genocide? Asking for a not friend.

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Amanda Warr @amandatron89.bsky.social · 25/03/2026

God it'd be so much funnier if he weren't in charge of anything and no one took him seriously.

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Amanda Warr @amandatron89.bsky.social · 25/03/2026

If your gut microbiome is plants, you're not having a good time.

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Amanda Warr @amandatron89.bsky.social · 18/03/2026

It has been an unpleasant few months, but the lymphoma is one of the curable ones, so with a little luck I'll be back to regularly scheduled life and science soon 🤞 Note: probably not Nature's fault, just regular old nature.

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Amanda Warr @amandatron89.bsky.social · 18/03/2026

6 rounds of chemo and 18 fractions of radiotherapy (ouch!) later I'm hopeful for an all clear soon. A big help to me has been Maggie's Centres who offered so much support. My friend and colleague Natalie Ring is raising money for them running 10k and we'd both appreciate any donations to the cause!

justgiving.com

Natalie is running 2026 EMF 10k for Maggie's Centres

Help Natalie Ring McBrien raise money to support Maggie's Centres

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Amanda Warr @amandatron89.bsky.social · 18/03/2026

Just over 8 months ago I was on here announcing the publication of my first Nature paper, exactly a week later I found a lump. A lump that alarmingly doubled in 24h. A very stressful few weeks later I was diagnosed with an aggressive lymphoma.

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Dr Emma Hodcroft @firefoxx66.bsky.social · 10/03/2026

1/5 Introducing SimPlot-CL! 🧬 Recombination plays an important role in viral evolution. Similarity plots are a great way to visualize recombination patterns, but generating them across many genomes can be cumbersome (Work with my student, Keno Strotjohann!) 📂 github.com/hodcroftlab/simplot-cl

A figure showing a 'Simplot' which plots the similarity of a genome to other genomes across a graph, with similarity on the Y-axis and the genome position on the x-axis. Many coloured lines show the sequences being compared - those closest to the top (similarity of 1) are the closest matches in different parts of the genome.

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NY Times Pitchbot @nytpitchbot.bsky.social · 14/02/2026

Doctors say that vaccines protect children from dangerous diseases. A nepo baby who barbecues dogs and snorts cocaine off toilet seats says that vaccines make children vulnerable to 5G radiation. For busy parents, it can be hard to know who to trust.

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Julie K. Brown @jkbjournalist.bsky.social · 01/02/2026

Troublemaker is my middle name.

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BK. Titanji @boghuma.bsky.social · 27/01/2026

There is a cost to science denial.

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Adam Kucharski @adamjkucharski.bsky.social · 25/01/2026

Quickly telling someone you’ve liked something they’ve done (e.g. telling a writer you like their writing, or a researcher you like their research, or a teacher you like their teaching) has a phenomenally high effort-to-impact ratio.

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Dimitri Drekonja, MD, MS @dimitridrekonja.bsky.social · 24/01/2026

Alex Pretti was a colleague at the VA. We hired him to recruit for our trial. He became an ICU nurse- I lover working with him. He was a good kind person who lived to help and these fuckers executed him. White. Hot. Rage.

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Amanda Warr @amandatron89.bsky.social · 20/01/2026

"I know we'll come to (Nato's) rescue, but I just really do question whether or not they'll come to ours"- Trump Mate, article 5 has been invoked exactly once and guess who it was in aide of...

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Amanda Warr @amandatron89.bsky.social · 07/01/2026

Not at the moment, seeing his neurologist today for some meds adjusting fun 🤞

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Amanda Warr @amandatron89.bsky.social · 06/01/2026

Very cool work! I have a cat with epilepsy and it is horrible. Awesome that Cronutt is cured and would be amazing for people suffering with epilepsy too 🤩

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Javier Santoyo @jsantoyo.bsky.social · 15/11/2025

OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis. #StructuralVariants #SVs #SVcomparison #SVidentification #Bioinformatics 🧪🧬 🖥️ academic.oup.com/bioinformati...

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