Gethsemane

7 dni temudiscuss

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-read advantage helps resolve some of those trickier regions

Gethsemane

7 dni temudiscuss

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 (rbcL + matK probably?). Worth having a look at how Plasmidsaurus did this, they did have a similar service for microbiome analysis (https://plasmidsaurus.com/sample-prep/microbiome#16S-extract... - looks like they don't accept raw samples anymore though...). Oxford nanopore sequencing is a decent technology for this as it's fairly straightforward to get working and easy to scale :) As an added bonus, you could perhaps also carry out 16S sequencing in parallel from the sample to get an idea of the microbiome of the sewer.

Gethsemane

w zeszłym miesiącudiscuss

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!

Gethsemane

w zeszłym miesiącudiscuss

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...

Gethsemane

2 miesiące temudiscuss

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)

Gethsemane

2 miesiące temudiscuss

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...

Gethsemane

2 miesiące temudiscuss

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

Gethsemane

3 miesiące temudiscuss

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.

Gethsemane

3 miesiące temudiscuss

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.

Gethsemane

9 miesięcy temudiscuss

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.

Gethsemane

9 miesięcy temudiscuss

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...

Gethsemane

9 miesięcy temudiscuss

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.

Gethsemane

10 miesięcy temudiscuss

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 :)

Gethsemane

11 miesięcy temudiscuss

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!

Gethsemane

w zeszłym rokudiscuss

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)

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