Hacker News: Gethsemane

New comment by Gethsemane in "I'm skeptical about efforts to revolutionize schooling"

Gethsemane — Fri, 05 Jun 2026 08:23:17 +0000

With AIs as teachers, I disagree. But with AIs assisting routine grading, filling in the university's assessment_framework_draft_v3_final_FINAL.docx, and otherwise freeing up time to actually focus on students - maybe? Although I fear that any productivity gains will be swallowed up by further reductions in lecturer headcount...

New comment by Gethsemane in "A New Typst Template for Pandoc (2025)"

Gethsemane — Thu, 28 May 2026 08:25:14 +0000

Very nice! I also like working from pandoc where possible - being able to split the output into a latex/typst file as well as a docx is very handy, especially when working with collaborators who are more comfortable with word. I wish markdown would see more support in scientific writing - it would solve so many of the headaches with formatting etc (and reduce microsoft's dominance in research)

New comment by Gethsemane in "Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop"

Gethsemane — Wed, 27 May 2026 20:28:17 +0000

Ultimately you're not going to find a service that can guarantee privacy, but your best bet might be to extract DNA at home (though tricky without a centrifuge etc...) and submit it to a standard sequencing provider novogene, plasmidsaurus etc. Realistically, they'll hold onto the data for a couple of months as part of the order, then delete it to clear up space. A bunch of discordant sets of DNA sequence without metadata isn't exactly useful for nefarious purposes! I wouldn't recommend sequencing at home unless you are very enthusiastic...

New comment by Gethsemane in "Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop"

Gethsemane — Wed, 27 May 2026 20:13:11 +0000

It's very context-dependent - the seqera rewrites so far seem to be pretty reliable, most of the work was spent merging the functions of multiple data QC tools into a single program (previously, there was a lot of redundancy that wasted compute). The success of other rewrites that I've seen tends to depend on the author's care/experience and usefulness. In my experience, bioinformaticians are fairly slow on the uptake of new software which might actually be an advantage here :-)

In defense of a lot of these bioinformatics-specific rewrites, there are some really dodgy coding practices and bugs that exist in well used tools, so there is scope for genuine improvement. The most recent release of minimap2 fixed some bugs identified in a rewrite, for example: https://github.com/lh3/minimap2/releases/tag/v2.31

New comment by Gethsemane in "GPT‑Rosalind for life sciences research"

Gethsemane — Fri, 17 Apr 2026 14:17:10 +0000

I somewhat agree, in that most of these life science adjacent demos are essentially "find good drug targets for $DISEASE", which mostly overfit to existing, well-classified drugs and targets. The biggest gains IMO will be in improved connectors with autonomous lab platforms, better sharing and annotation of relevant data sets, and yes also improving the pathway to clinical trials.

At the moment, it feels like releases like this overcommit and overpromise on "PhD level reasoning", which I wouldn't say is the absolute bottleneck in clinical research.

New comment by Gethsemane in "Silicon Valley is turning scientists into exploited gig workers?"

Gethsemane — Fri, 17 Apr 2026 13:47:31 +0000

It's also all too easy to arbitrarily label something as "bureaucratic" and demand that it gets razed and rebuilt. I'm sure Palantir has some level of bureaucracy internally with all the new contracts it has won - perhaps we should also rip that apart?

Fact is that a university that must simultaneously handle education, research, publishing, estate management, legal stuff, media coverage, health and safety etc etc etc ends up being somewhat bureaucratic.

New comment by Gethsemane in "Meow.camera"

Gethsemane — Fri, 17 Oct 2025 10:05:02 +0000

A highlight of my time in Turkey was the cats - thank you for your efforts! Antalya had a lot of cat hotels in the park and most looked very healthy.

New comment by Gethsemane in "Apple M5 chip"

Gethsemane — Wed, 15 Oct 2025 14:44:25 +0000

If I was less lazy I could probably find this answer online, but how do you find the battery life these days? I'd love to make the switch, but that's the only thing holding me back...

New comment by Gethsemane in "OpenZL: An open source format-aware compression framework"

Gethsemane — Mon, 06 Oct 2025 21:27:17 +0000

I'd love to see some benchmarks for this on some common genomic formats (fa, fq, sam, vcf). Will be doubly interesting to see its applicability to nanopore data - lots of useful data is lost because storing FAST5/POD5 is a pain.

New comment by Gethsemane in "Removing newlines in FASTA file increases ZSTD compression ratio by 10x"

Gethsemane — Mon, 15 Sep 2025 14:49:19 +0000

Unfortunately, when you write a program that doesn't wrap output FASTAs, you have a bunch of people telling you off because SOME programs (cough bioperl cough) have hard limits on line length :)

New comment by Gethsemane in "Do I not like Ruby anymore? (2024)"

Gethsemane — Tue, 26 Aug 2025 12:29:14 +0000

I really want to like typer, and frequently go down the rabbit hole of rewriting all my argparse into typer, but I keep getting put off by it's high import cost and that development seems to be a bit up in the air (see https://github.com/fastapi/typer/issues/678#issuecomment-319...). A shame because otherwise it's a really nice library!

New comment by Gethsemane in "AlphaGenome: AI for better understanding the genome"

Gethsemane — Thu, 26 Jun 2025 20:48:41 +0000

Agreed, there’s been some interesting developments in this space recently (e.g. AgroNT). Very excited for it, particularly as genome sequencing gets cheaper and cheaper!

I’d pitch this paper as a very solid demonstration of the approach, and im sure it will lead to some pretty rapid developments (similar to what Rosettafold/alphafold did)

New comment by Gethsemane in "Using Pandoc and Typst to Produce PDFs"

Gethsemane — Fri, 29 Nov 2024 14:08:53 +0000

Something I found useful is that you can create a much more minimal pandoc template for typst than for latex. Obviously if familiar with latex it probably won't be an issue, but when I tried to make my own barebones pandoc template (i.e., stripping out beamer) I gave up.

New comment by Gethsemane in "Using Pandoc and Typst to Produce PDFs"

Gethsemane — Fri, 29 Nov 2024 14:07:16 +0000

I've similarly found the combination of pandoc + typst to be quite exciting. I've found it particularly useful for typesetting academic papers - I'm quite averse to word in general, don't require extensive mathematical typesetting support, and find latex to generally be quite unapproachable (just look at the size of the default pandoc template!), and so it gives me a method of making a decent pdf whilst simultaneously producing a .docx for my collaborators. Being able to track changes with git is also a huge advantage, although never had the chance to work with someone who is comfortable using git :(

The recently added support for PDF/A is also quite exciting, as I've never found a satisfactory solution to this with latex. Now I just wish journals would support markdown submissions...

New comment by Gethsemane in "Chemists Create World's Thinnest Spaghetti"

Gethsemane — Mon, 25 Nov 2024 19:06:09 +0000

I am a fan of the colour scheme they selected in figure 2 - very relevant. https://pubs.rsc.org/image/article/2024/na/d4na00601a/d4na00...

New comment by Gethsemane in "Hoodmaps: Publicly Annotated City Maps"

Gethsemane — Thu, 26 Sep 2024 15:01:59 +0000

As an example of a more informative map of income/deprivation, I recently encountered the Scottish Index of Multiple Deprivation website (https://simd.scot). Only applicable to Scotland (obviously), but it is interesting to see how each city is a mosaic of social status. From personal experience, it is extremely accurate down to the street level!

New comment by Gethsemane in "How I Built My Blog"

Gethsemane — Wed, 25 Sep 2024 12:26:36 +0000

50% CPU usage on the home page, and the firefox inspect tool crashes before it can open! The content itself doesn't load either - just a large blue box

New comment by Gethsemane in "LinkedIn is now using everyone's content to train their AI tool"

Gethsemane — Thu, 19 Sep 2024 09:33:54 +0000

It is a shame. Twitter used to be quite a popular platform for (useful and interesting) networking in academia, but after it began to fall apart everyone started looking for alternatives. I felt that LinkedIn should be a decent alternative as it could strike that balance between professional and personal content, but there is just no way for a genuine community to develop on LinkenIn in its current form.

Even now LinkedIn is possibly the worst platform for being polluted with "AI slop", I cannot understand why they are looking to advance this further. Hell, when you go to write a post now there is a big flashing button saying "USE AI TO WRITE THIS POST"...?!?!

New comment by Gethsemane in "Why wordfreq will not be updated"

Gethsemane — Wed, 18 Sep 2024 19:20:10 +0000

Sounds like your laptop is wholly out of date, you need to buy the next generation of laptops on Amazon that can handle the modern SEO load. I recommend the:

LEEZWOO 15.6" Laptop - 16GB RAM 512GB SSD PC Laptop, Quad-Core N95 Processor Up to 3.1GHz, Laptop Computers with Touch ID, WiFi, BT4.2, for Students/Business

Name rolls off the tongue doesn’t it

New comment by Gethsemane in "React for R"

Gethsemane — Wed, 18 Sep 2024 10:12:47 +0000

I agree that it's perhaps not the most robust choice, but at least for my field (bioinformatics) it's a good balance between accessibility and performance. That being said, in most cases when I come across a paper >1 year old presenting the latest-and-greatest Shiny web app, it is wholey broken when I try to use it :|