I never understood why so many men associate with imagery of predatory animals.

My idealized version of my own masculinity is best represented by a tree. Patient. Immensely endurant. Self-sufficient. Unbothered by trivial, ephemereal affairs. Innately kind to the world around it.

I don't want to be a lion or a wolf or a shark, I want to be an ancient oak whose branches have sheltered countless birds and squirrels.

@luzkenin @selfhst that looks like a great resource, thank you! Would you also haplen happen to be aware of "newcomer guides" that explain the basics self-hosting?

I feel proficient in shells/DBs/unix environments, but am unsure how much work it will be to get all moving parts to behave nicely with each other. An overview guide might be really helpful there.

Finally want to embark on moving to #selfhosted services. Any recommendations for blogs written by humans instead of AI slop? Pointers to software and hosting solutions also appreciated!

Ideally I'd move email and cloud backups such a photos over. Been thinking of setting up #nextcloud alongside a backup DB on the same host.

#selfHost

@eliocamp seeing as your profile suggests you are used to R, you might like plotnine which gives ggplot2-like syntax. What's really missing is all the extensions to ggplot2, but of course it's impossible to port them all.

Samples from asteroid Bennu contain A, G, C, T & U nucleotide bases, and 14 of 20 amino acids used by life — but while we use only left-handed versions of these molecules, Bennu has a roughly equal L/R mixture, puncturing theories that the bias on Earth came from an initial cosmic seeding.

https://www.nature.com/articles/d41586-025-00264-3

@lwpembleton if it's just a data directory I sometimes also include source.txt with the download URL. If it's a whole project, README.md all the way.

How do you balance priorities during job hunts? Specifically tradeoffs in personal growth, work conditions, and ethical considerations?

Looking for any experiences and dillemas you may have faced and how you tackled them.

#JobHunt #discussionwelcome

@willmcgugan great to see this out! I used textual earlier this year to have a quick, human-friendly interface to our cluster management system. Developing the frontend took a fraction of the time needed for the backend, which was a delight for someone like me that never does frontend! Super useful, thanks for making it!

The problem of fake science papers when trying to write a systematic review https://www.science.org/content/article/systematic-reviews-aim-extract-broad-conclusions-many-studies-are-peril

@lwpembleton yeah prices for grinders can be absolutely insane. I'd say that, unless you need a really good grind for an espresso machine or a specific taste, the C2 (or newer models) will be plenty. If you're in no rush they're quite affordable on aliexpress.

@lwpembleton I've been quite happy with my Timemore C2, but don't have the fanciest brewing method - just a trusty Bialetti Brikka. I wouldn't go for this mill if you're gonna switch to an espresso machine, but for anything that's not espresso-grade fine I think it's a great mill.

If you're like me and use the scverse (scanpy, anndata and the like) a lot and need to pseudo-bulk every once in a while, you may have missed that scanpy now ships with built-in functionality for that: https://scanpy.readthedocs.io/en/stable/generated/scanpy.get.aggregate.html
Very useful!

@simontatham yea this is why I post this kind of thing, I want to show it's normal to not know stuff :)

@PhilippBayer A Seqera rep told me they're working on a linter/parser to improve developer experience and catch those things before they cause incomprehensible error messages. I don't see a prototype online yet, though. But Amazon seems to work a bit in that direction: https://github.com/awslabs/linter-rules-for-nextflow

@Psy_Fer_ for me it's being stuck on an old CentOS with horribly outdated compilers. Having everything precompiled is an enormous advantage over figuring out after the fact that your compiler toolchain is outdated. Especially if you don't have the rights to change that.

@PhilippBayer this is super cool and makes me wonder how cheaply one could ID foraged foods. I guess running an ONT is still not exactly cheap for most, but maybe if one had a targeted panel of some sort?

@lwpembleton @danwwilson I find that often when using institution colors it's more about illustrative purposes and less about good data viz (otherwise one would use appropriate palettes). For such an example, see https://github.com/hwarden162/HGUTheme

And that's the kickoff of the scverse conference 2024, hosted by @scverse
First keynote by Rob Patro @nomad421 who shows concerning discrepancies between results obtained with different versions of CellRanger and pitching the shiny alevin-fry framework instead.

New preprint!

The radial positioning of genomic loci, i.e. how far they are from the nuclear lamina has been associated with genome structure and function for several decades.

But in genomics everything is correlated, e.g. radial positioning with genomic compartments with gene activity etc

@gdagstn completely agree. It's good for running the defaults, but when I want to understand what's happening under the hood I find myself jumping into their source code a lot more than I do for other software. I suppose it's difficult making a one size fits all solution (that is good for wetlab and drylab researchers).