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John Marshall

@johnm.bsky.social
959 followers 318 following 319 posts

Bioinformatics tools developer at Australia’s Centre for Population Genomics. Will edit GA4GH specifications for food. New Zealander fairly recently returned after a decade in the U.K.

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Reposted by John Marshall
Paul Le Comte 🇳🇿🇨🇦📷 @paullecomtephoto.nz · 22/09/2026
Seacliff farm sheds, North Dunedin #Nikon #Rural I've always been a fan of this fangled new 'hyper localism', a reaction to 'influencer photographers' all travelling to the same insanely beautiful 'secret' location to get iconic shots. Celebrating the local rocks my boat too
A shed north of Dunedin. Loving 'hyper localism' - celebrating the local instead of the iconic influencer photography
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Felix Geiringer @barristernz.bsky.social · 22/09/2026
I'm at Unity Bookshop Wellington for the Nicky Hager book launch. The event is not due to start until 6 pm, but the room is mostly full already and filling up fast.
Unity Bookshop filling fast.
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John Marshall @johnm.bsky.social · 16/09/2026
Investigating pysam wheel sizes had been on my to-do list for a while. Recently realising that we'd used 6 GiB out of our default 10 GiB PyPI limit and had room for maybe five more releases made it urgent. Last week's 0.24.1 release reduces the per-release total from ~760 MiB to ~150 MiB. 🧬🖥️ 🧵
Bar chart showing total release sizes gradually increasing from 2021's version 0.17.0 to a peak of 760 MiB for the second most recent release (2026's 0.24.0) before dropping to ~150 MiB (between 0.17.0 and 0.18.0 in total size) for the most recent release.

Interesting discontinuities are 0.22.0, which added ARM wheels for macOS, and 0.23.1, which added musl Linux wheels. The sdists are ~5 MiB making a barely visible blue sliver at the bottom of the graph.
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John Marshall @johnm.bsky.social · 07/09/2026
Today's pysam 0.24.1 release bundles htslib, samtools, and bcftools 1.24 and has pre-built wheels on PyPI for Python 3.9 through 3.15. Wheels are much smaller than in previous releases. It includes type hint fixes, some speed optimisations, and a new reverse_complement() utility function. 🧬🖥️
github.com
Release v0.24.1 · pysam-developers/pysam
This minor pysam release wraps htslib/samtools/bcftools version 1.24. It has been tested with Python versions 3.9 through 3.15 (RC2) and wheels are available via PyPI for all of those Python versio...
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John Marshall @johnm.bsky.social · 05/09/2026
Probably the biggest organisational change we've made in pysam for a while: Dynamically load libcurl and libcrypto in order to subvert Linux wheel repair and avoid these libraries being bundled into the final wheels. (This organisational change affects only the pre-built Linux wheels.)
github.com
Prevent libcurl/libcrypto/et al being bundled in Linux wheels by jmarshall · Pull Request #1420 · pysam-developers/pysam
An alternative to PR #1415 which reapplied the CA bundle location hack to hfile_s3.c. Because Linux wheels bundle libcurl.so and are built on AlmaLinux (i.e., a Red Hat flavoured distro); and becau...
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John Marshall @johnm.bsky.social · 02/09/2026
A week later, and no response from my electorate MP other than the autoreply from her office. I also emailed Reuben Davidson asking if the public are allowed to read his reported “79 questions” letter… 🦗🦗 Labour really working hard to earn every vote here… 🙄
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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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John Marshall @johnm.bsky.social · 27/08/2026
Days since I've been screwed by SELinux: 0 I spent years reflexively removing the selinux packages whenever I upgraded Fedora. Was hoping not to have to go back to that…
bugzilla.redhat.com
2502040 – ssh agent forwarding blocked by selinux debug1: Remote: Agent forwarding disabled: couldn't create listener socket
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Morgan Davie @fromthemorgue.bsky.social · 26/08/2026
Just reflecting on the fact that when a Kiwi was seized and detained for weeks by the US regime, our Minister of Foreign Affairs (who also leads a party in govt) responded by sharing an elaborate and obvious lie that it was her own fault- -and it has disappeared down the memory hole already. 1/
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Dr. Cassandra Mudgway @legallyfeminist.bsky.social · 24/08/2026
I read 54 pages of draft legislation so you don't have to. Important notes: this is not "systemic change" as there's no obligation to make platforms (or AI companions) safe. There's no ref to gender based violence, children's rights, or te Tiriti. It's an age ban and a duty to assess risk. #nzpol
Meme where the govt slaps "age ban" on a leaky water cooler labeled social media harm.
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David Hood @thoughtfulnz.bsky.social · 24/08/2026
What I have spent the last hour writing.
As you are my local MP, I am writing to encourage you, and Labour, not to support National’s Online Safety (Minimum Age and Child Safety Risk Assessment) Bill. 
This is a bill that both does not address the problem it is trying to solve, and restricts legitimate democratic organisation of under 16 year olds.
A central issue is that the law initially defines platforms by harmful features, but then exempts whole classes of services according to their stated primary purpose. A messaging or gaming platform may still contain recommender systems, public or semi-public communities, direct contact with strangers, disappearing messages, engagement feedback, commercial profiling, in-game purchases, or other harmful features.
The available NZ evidence [1] [2] identifies harm through content, contact, conduct, commercial practices, and platform design, not simply through conventional social-media feeds. 
So the sources of harm identified targeted in the National’s proposed law are not the sources of harm actually being reported by young people. This exemptions method is not fit for purpose.
Academic work has also shown that young people use social media to poltically organise for causes of interest [3], and early evidence from the Australian ban is among under-16 users whose social-media use was significantly disrupted, 51% reported receiving less news as a direct result. Those affected also reported fewer opportunities to discuss news and issues that mattered to them [4].
I think it is part of Labour’s values that young people of the opportunity to participate in society, so that they are active particpants of society as adults.

Not room in alt text for references
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Andrew @openpolicy.bsky.social · 24/08/2026
The NZ Herald reports the bill will be discussed at the Labour Party's parliamentary caucus meeting tomorrow (Tuesday 25 August), so it's important to let Labour MPs know how you feel about the Bill today. List of Labour MPs here: www3.parliament.nz/en/mps-and-e... #nzpol
www3.parliament.nz
Members of Parliament - New Zealand Parliament
Find out who the current MPs are, including their roles and responsibilities. This section also shows you where they sit in the House and how to contact them at Parliament.
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NZ Council for Civil Liberties @nzccl.org.nz · 24/08/2026
Very disappointed to see the govt proposing a ban on under-16s using social media. While we agree there is work to be done, a ban is the wrong approach and interferes with young people's rights to communicate with family, each other, and the wider world. www.rnz.co.nz/news/politic...
rnz.co.nz
Watch live: Govt pushes ahead with social media ban for under-16s
The government is pressing ahead with its ban on social media for under-16 year olds, with the legislation set to be introduced on Monday.
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John Marshall @johnm.bsky.social · 24/08/2026
Surely (surely…!) Labour would not offer support to the government on a contentious topic less than three months before an election. I've told my Labour MP what will happen to my vote if the party supports this, and I hope they get a deluge of such letters.
Letter emailed to MP:

I see from the news today that the government finally plans to move ahead with its proposed social media ban for those under 16. RNZ reports that ACT and New Zealand First will not support this bill, and that National will therefore need Labour's support for the bill to progress.

Such bans are ill-considered and I trust Labour will not support the National Party in this. Both on its (lack of) merits, and because it is far too close to the upcoming election for Labour to be supporting any government legislative action. If Labour were to support this bill, I would not be able to support a Labour electoral candidate or the party with my vote in November. As a voter, I am sure I am not alone in this conclusion.

For further background on alternatives to such bans, I would commend to you InternetNZ's submission in response to the Education and Workforce Committee's inquiry in 2025:

[URL follows.] https://internetnz.nz/assets/Archives/Submissions/InternetNZ-Submission-on-Inquiry-into-the-roles-can-the-Government-business-and-society-can-play-in-addressing-online-harms-to-New-Zealands-youth-25-July-2025.pdf
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joel @jmoonz.bsky.social · 23/08/2026
Wait what, synthID requires access to the secret key used to encode the watermark? And we just have to trust the person with the secret to say yes or no? I know DRM is pretty useless, but this is next level useless.
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Dan Kaszeta FRHistS @dankaszeta.bsky.social · 13/08/2026
There was no cholera in ancient or medieval Europe; it’s a 19th century arrival to Europe
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John Bull @garius.bsky.social · 13/08/2026
Spot the literal criminal offence.
trending column on Bluesky proclaiming a false result for a UK election happening today.
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John Marshall @johnm.bsky.social · 13/08/2026
Last year 2785 people voted in the InternetNZ Board election, and 1046 (37%) of them had an FSU candidate as their first preference. This year 3104 people voted, 1923 (61%) of them for an FSU candidate as first pref. Very unevenly: Brown had 1822 (58%) of the first prefs and—go figure—was elected.
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Kate Pearce @secvalve.bsky.social · 13/08/2026
Let this remind you that what matters in democracy is. - enrolling to become eligible to vote - turning up to vote - casting a valid and effective vote
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John Marshall @johnm.bsky.social · 13/08/2026
First #InternetNZ AGM motion vote at 7.30, scheduled for a minute or two after 6:55 — we're only running half an hour late after two hours elapsed!
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John Marshall @johnm.bsky.social · 13/08/2026
Currently ~900 people in the InternetNZ AGM meeting. Early days yet, still just testing the voting system — if memory serves, we spent AGES doing this last year!
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Nabil Sabio Azadi @nabilsabioazadi.bsky.social · 12/08/2026
Tēnā koutou, e hoa and #InternetNZ folks! Here are my thoughts on Motions 2–5 and Motion 9, and what they could actually require of Ipurangi Aotearoa: bit.ly/3St9A2E.
bit.ly
7HrMgK8pkmYZu1Rytv1W | Riseup Pad
A collaborative document that everyone can edit in real time.
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David Slack @davidslack.bsky.social · 12/08/2026
It's going to be proper Red Wedding if it's Winston who comes out
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John Marshall @johnm.bsky.social · 12/08/2026
Live from the prime ministerial lectern! It's riveting stuff…
Radio New Zealand's livestream: “The Prime Minister is due to address media at 12.35pm. Watch a livestream of the announcement…”

It's an empty lectern at 12:40pm.
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John Marshall @johnm.bsky.social · 11/08/2026
Late addition motion 9 #InternetNZ. You Cannot Be Serious. (And once again the apparent FSU stooge feels no need to provide any supporting information explaining why their onerous suggestion might be worthwhile.)
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Tim @timward2014.bsky.social · 10/08/2026
Electoral Commission: We tried and failed to get hold of the voter, so we moved them to the dormant roll. The voter? Labour MP Willow-Jean Prime, just in case you were wondering who is being targeted by roll-cleansing… #nzpol www.rnz.co.nz/news/politic...
rnz.co.nz
Labour MP among 115,000 NZers currently on dormant electoral roll
Labour MP Willow-Jean Prime is sounding the alarm after discovering she was moved on to the dormant electoral roll earlier this year without her knowledge.
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Jonathan Brewer @kiwibrew.bsky.social · 10/08/2026
I proposed an amendment to the Internet NZ Constitution that's up for vote at the AGM this Thursday. I proposed a Nominating Committee, or a NomCom, a standard practice across the world's Internet Governance structures. Members can register for the AGM here: internetnz.zoom.us/webinar/regi...
internetnz.zoom.us
Video Conferencing, Web Conferencing, Webinars, Screen Sharing
Zoom is the leader in modern enterprise video communications, with an easy, reliable cloud platform for video and audio conferencing, chat, and webinars across mobile, desktop, and room systems. Zoom ...
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Terry Baucher @trabaq.bsky.social · 09/08/2026
Mōrena e te whanāu fog blanketed most of Rangitoto and the North Shore this morning but it made for a dramatic view from the top of Maungauika. Once it lifts it should be a fine day ahead here in Tāmaki Makaurau. Kia pai tō rā!
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Cynethryth @cynethryth.com · 09/08/2026
Vote by 12pm today for #InternetNZ board elections!! Don't forget! And don't forget to sign up for the AGM! Last year, about 1/3 of the voters were FSU, so if you don't want bad motions to pass, come in numbers! Order a pizza! Chill on Bluesky. Make an evening of it!
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Dylan Reeve @dylanreeve.com · 09/08/2026
TODAY is your last chance to vote in the InternetNZ board election! Like, now. If you are a member and haven't voted, then now (like right this moment ideally) is the time to do so! The instructions will be in your email.
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Kay in the End Times 🏳️‍🌈 💗💜💙📚 @jennykaynz.bsky.social · 09/08/2026
Reminder #InternetNZ members, voting closes 12noon on Monday 10 August! That's tomorrow! 🗳 It's STV voting so give your 1 and 2 to candidates you most want to see on the board. Number others you're OK with. Number last or not at all those you actively distrust or have concerns about. 🥇🥈🥉⬛
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John Marshall @johnm.bsky.social · 06/08/2026
The clock has started… Python 3.15rc1 was released on Tuesday which freezes the Python ABI, and the same day's cibuildwheel release now builds 3.15 wheels by default. The 3.15 release proper is expected in early October. We shouldn't have too much trouble getting a pysam release out before then.
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John Marshall @johnm.bsky.social · 05/08/2026
The recording of the #InternetNZ Meet the Candidates session is now available at www.youtube.com/watch?v=ion_... (via an announcement on NetHub this morning)
youtube.com
Meet the Candidates | InternetNZ Board elections 2026
YouTube video by InternetNZ | Ipurangi Aotearoa
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Andrew @openpolicy.bsky.social · 04/08/2026
How about a journalist asks Erica Stanford to explain what the “legal reasons” are why she “can’t” share a copy of her Social Media Ban (Forced Online Identification for All) Bill? In a sensible country this bill would’ve been preceded by consultation on a draft bill. www.rnz.co.nz/news/politic...
rnz.co.nz
National wants to show Labour the social media ban bill, but 'we can't', education minister says
The education minister says she hopes to get a copy of the social media ban bill to Labour's caucus this week, after previously saying legal reasons were preventing her from doing so.
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Emma Hart @ghet.bsky.social · 04/08/2026
Let me take a minute to tell you how bonkers this is. The first election I worked was (I think) 2008, before there was really any advance voting. At every election, if you weren't on the roll, we let you cast a special vote and then worked out if you were eligible afterwards. Two reasons: 1/2
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Jonathan Brewer @kiwibrew.bsky.social · 04/08/2026
I've open-sourced another new container-based API tool this week for calculating a viewshed anywhere on earth using Corpernicus WorldDEM-30. github.com/InternetSoci...
github.com
GitHub - InternetSociety/glo30: Copernicus DEM GLO-30 Terrain Analysis API Server
Copernicus DEM GLO-30 Terrain Analysis API Server. Contribute to InternetSociety/glo30 development by creating an account on GitHub.
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Jim Waterson @jim.londoncentric.media · 02/08/2026
more good content! imagine publishing content that's just nice! reveals a little bit about having fun on the internet! people just doing things because they can and the internet was nice!
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Dr Sarah Hendrica Bickerton 🏳️‍🌈 @sarahhbickerton.bsky.social · 30/07/2026
I was listening to @bernardchickey.bsky.social's 'The Hoon' podcast this morning, and I must say I agree very much with Helen Clark (always find it amazing that her Bluesky account is suspended) that Winston Peters should be sacked as AoNZ Foreign Minister. thekaka.substack.com/p/the-weekly...
thekaka.substack.com
The Weekly Hoon: Helen Clark on why Winston Peters should be fired over his 'go home' comments, & on NZ's humiliation on a key UN vote
Bernard Hickey, Peter Bale & Cathrine Dyer discuss the week in geopolitics, the economy & climate; plus special guests Helen Clark & Janet Anderson on NZ's UN vote, the ICC & Winston's 'go home' jibe
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John Marshall @johnm.bsky.social · 30/07/2026
TIL Python's subprocess.run() et al routines have a cwd parameter that specifies a directory for the command to run in. I foresee a lot less writing of directory-changing context managers in my future… (Well, a reduction from inherited 1 + wrote 1… …to zero.)
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John Marshall @johnm.bsky.social · 24/07/2026
Considered asking one of the #InternetNZ Board candidates just what involvement she is thinking of in her statement “I believe Internet New Zealand’s involvement in assessing some views as misinformation/disinformation should be anathema for a regulator”… …but Do Not Engage is a better policy.
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Ryan Wiley @rdubwiley.bsky.social · 22/07/2026
I simultaneously think AI psychosis is often caused by deeper underlying causes (rather than just exposure to the technology) while also thinking the massive disruption to coding as a lifestyle is giving an entire generation of engineers mental health issues.
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Stephanie Rodgers 🍉 @bootstheory.bsky.social · 18/07/2026
It's actually antidemocratic for our media to be so uncritical about basic, commonly understood political agendas at this point Explaining politics *is your goddamned job*, you shouldn't need to have *basic context* suggested by a member of the public.
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Smashshitupika @shambolika.bsky.social · 14/07/2026
I've known Paul Henry is dodgy since I was a teen in my dad's antique shop; Paul waited until my dad was out, then told me "Gary said I could have $50 off of this" and I was very naive, believed him. He know it was a small town, that my dad would tell people Paul's a dick but he didn't care...
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John Marshall @johnm.bsky.social · 13/07/2026
Slightly surprised to look again at my bio and see that I did indeed put the word “bioinformatics” in there…
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John Marshall @johnm.bsky.social · 09/07/2026
“Why do you always try to merge bioconda samtools et al updates yourself, John?” Due to inline functions, merging the bioconda htslib/samtools/bcftools PRs fully correctly is not as straightforward as it looks. These releases occurred at 3am in my time zone and someone else got to them first… 🫠
github.com
Update htslib to 1.24 by BiocondaBot · Pull Request #67046 · bioconda/bioconda-recipes
Update htslib: 1.23.1 → 1.24 Info Link or Description Recipe recipes/htslib (click to view/edit other files) Summary C library for high-throughput sequencing data formats. Home https:/...
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Andrew Whitwham @whitwham.bsky.social · 09/07/2026
Release 1.24 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See htslib.org/download/ for links to tarballs and release notes. 🧪🧬🖥️
htslib.org
Samtools
Samtools
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Shuangjia Lu @lushjia.bsky.social · 07/07/2026
🔥 Does switching to a pangenome reference actually improve your association study? We tested it, and the answer is yes, measurably. Our preprint is online now: "Pangenome-based human genome analysis improves trait association and genomic prediction": doi.org/10.64898/202...
doi.org
Pangenome-based human genome analysis improves trait association and genomic prediction
The Human Pangenome Reference Consortium has generated 462 open-access reference genomes and a variation graph that represents differences among them, providing a substrate for pangenome-based analysi...
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Kieran @nugmonster.cryptoanarchy.network · 07/07/2026
On the 12th of feburary, Paul Goldsmith had two meetings, one with the free speech union, and one with the human right's commission. I submitted an OIA for documents relating to those two half hour meetings, and apparently that was such an onerous request, Goldsmith requested an extension in order
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