Jochen Weile @jweile@qoto.org

Now out in @AnnualReviews of Genetics!!

We review the use of functional assays for the study of human coding and noncoding SNVs, exploring current applications and outlining key methods and principles of experimental design.

An enormous thank you to Victoria Parikh, Prashant Mali, Fritz Roth (@fritzroth), and Melina Claussnitzer who I count myself very lucky to have worked with!!

And a thank you to the AVE ETS working group and of course, to @AnnualReviews!

http://www.annualreviews.org/eprint/TK7RFGUFU64ZEAI6UPW4/full/10.1146/annurev-genet-072920-032107

https://www.bakerlab.org/2022/11/30/diffusion-model-for-protein-design/ " A diffusion model for #protein #design (...) Highlights include a picomolar binder generated through pure computation and a series of novel symmetric assemblies experimentally confirmed by electron #microscopy." #DALLE #IA

function box() { t="$1xxxx";c=${2:-=}; echo ${t//?/$c}; echo "$c $1 $c"; echo ${t//?/$c}; } # Make box around text. By bartonski
I made an explanation of how this works a while ago here: https://www.youtube.com/watch?v=9bZ85aMuf6c

Question: If you have a little R package floating around on github with a few useful functions that other people are using, where would you publish it to be "citeable"?

(I don't have the strength or patience to send it to CRAN.)

🚨 BIG EXOPLANET NEWS! 🚨

Our team has released FIVE papers today on the most COMPREHENSIVE study of an #exoplanet atmosphere to date!

Using #JWST we obtained four transit observations of #WASP-39b early in the telescope's operations to study both the planet itself, and the telescope's capabilities to observe exoplanet atmospheres.

We detected numerous molecules in the planet's atmosphere, including CO2, CO, H2O, and SO2 🧵

The future is here! ⭐ 🪐 🔭 #Astrodon #Science

https://webbtelescope.org/contents/news-releases/2022/news-2022-060

The duf is a better 'df' command. It gives you a single tool for checking disk usage and free space on Linux, macOS, *BSD, Windows, Android and Unix. Try duf today
https://www.cyberciti.biz/open-source/command-line-hacks/duf-disk-usage-free-utility-for-linux-bsd-macos-windows/

A reminder for anyone new to mastodon who might not be happy with some of the racist and bad actors out there on other servers... Just import the fediblock list to your personal blocks and you will be safe from the vast majority of bad actors.

Some Mastodon thoughts, for bird-site expats (which include myself). I'm aggregating these from posts I've boosted before, so little of this is my own brain.

- There's no algorithm here. That means favoriting/liking doesn't do anything except communicate approval to the OP and others (which is still nice!).

- No algorithm means boosting ("retweeting") is the true method to increase a post's visibility. Do that more than you did on birdsite.

- There's no post-quoting here, and that's by design. Look at quote-tweets on the birdsite; it's a feature primarily used for toxicity.

- There's no direct word-search here either; that means you want to use hashtags to make posts more searchable. This is also intended, since word-searching posts was often used to harass/stalk on the birdsite and elsewhere, so that was left by the wayside here. This also means hashtags are much more a thing here than any of the algorithm-powered sites.

- It's encouraged to put in text descriptions when you post images; a lot of Mastodon users use screen-readers due to various disabilities, and getting an image description read out loud helps them immensely.

- Speaking of screen-readers: using capitalization in your hashtags allows the screen-readers to read them more easily, especially if you're smashing multiple words together. #rockmusic = unreadable. #RockMusic = readable.

- The best way to make threads is to make set your first post as public, but "unlist" all of your replies. This prevents your whole thread from clogging up feeds.

- Content Warnings should be used more liberally here. If you haven't gotten the impression yet, much of Mastodon was built and populated by marginalized groups who were harassed/bullied off of other platforms. This is the culture they built, to respect each other's mental health. It's not a rule, but it's well-appreciated.

- Consider chipping a few bucks towards whomever runs the server you're on; the strain is real, and most server admins were likely paying out of pocket before so don't have an existing donation base. The growth here has been extremely fast, and that means money's needed.

- DMs are just posts with privacy settings. So if you @ someone in a DM, you pull them into the thread. That could be embarrassing.

- Also, no, DMs aren't end-to-end encrypted, but they aren't on Twitter either. Don't use either if you want true privacy.

- Including your Mastodon handle in your birdsite profile will help people find you here; there's a tool (pruvisto.org/debirdify/ is one of them that's used) people can use to pull Mastodon handles from Twitter profile.

- Use the blocking and reporting features liberally, if needed. This should go without saying, but they work, and work well!

- If there's an entire Mastodon server you don't want to hear from, you can block the whole thing too.

- Preferences -> Appearance -> "Slow Mode": this can make larger "Local" feeds and any "Federated" feed much more readable.

I'll reply with some more as I see them, or reply here too. I've only been here 4 days but I'm loving it so far.

Early adopter?

The Donnelly Centre @ University of Toronto is hiring 3 (❗) tenure-track positions in computational biology & functional #genomics.

Learn more about the positions & how to apply here: https://bit.ly/DonnellyRecruitment2022

Applications close January 16, 2023.
#bioinformatics #job

This looks exceptionally interesting:

"A structural biology community assessment of AlphaFold2 applications"

#StructuralBiology #Crystallography #CryoEM #ML

https://www.nature.com/articles/s41594-022-00849-w

#Macademia

Building an aggregator for #ScienceMastodon. Let's you view multiple servers at once. Creating a list of all the science servers I know of. Please let me know of any others!

genomic.social
ecoevo.social
mstdn.science
fediscience.org
scicomm.xyz
scholar.social?

Any others?