Gethsemane

6 ms·

1.
by Gethsemane 2mo ago
For most DNA it now sits at ~Q20 (1%) which is a big improvement - there was also some hacky stuff like HERRO and duplex sequencing which improved it substantially. For routine genome sequencing it's definitely suitable, and the long-r
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by Gethsemane 2mo ago
Fastest/cheapest sequencing based method would likely be to collect samples in DNA preserving agent (zymo DNA shield is decent for this), then have an automated platform for extracting DNA and preparing amplicon sequencing libraries (r
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by Gethsemane 3mo ago
Have you written about your experience anywhere? It would be interesting to see how you approached the research sector as a layperson. Are there any plans to move to in vivo? Best of luck with your research!
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by Gethsemane 3mo ago
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
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by Gethsemane 4mo ago
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 m
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by Gethsemane 4mo ago
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, plasmidsa
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by Gethsemane 4mo ago
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 waste
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by Gethsemane 5mo ago
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 impro
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by Gethsemane 5mo ago
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 - perhap
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by Gethsemane 11mo ago
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.
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by Gethsemane 11mo ago
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...
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by Gethsemane 1y ago
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.
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by Gethsemane 1y ago
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 :)
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by Gethsemane 1y ago
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:/&#x
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by Gethsemane 1y ago
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, an
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by Gethsemane 2y ago
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.
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by Gethsemane 2y ago
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 t
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by Gethsemane 2y ago
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...
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by Gethsemane 2y ago
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
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by Gethsemane 2y ago
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
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by Gethsemane 2y ago
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
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by Gethsemane 2y ago
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
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by Gethsemane 2y ago
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 p
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by Gethsemane 2y ago
Shiny is an R package that is quite popular for building data analysis web tools, I suppose this would be a useful extension for it! Despite R tending to give people 'the ick' it regardless seems to have become quite a solid platf
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by Gethsemane 2y ago
On the latest iOS update, searching for the Files app also returns a shortcut to the scanner. Weirdly, searching for "scan" or similar doesn't return it... The icon is similar in design to the control centre so you'd thi
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The biology of smell is a mystery – AI is helping to solve it(nature.com)
2 points by Gethsemane 2y ago|0 comments
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by Gethsemane 2y ago
It does seem like a bit of an unfair comparison. That being said, I am not aware of any k-mer python packages that have great performance. If k-mer counting performance was really important, I'd probably start to think about reaching