Apple pie @applepie@qoto.org

Boost this to enrage a chemist

Hey #bioinformatics folks!

I'm trying to create a subject and celltype-specific single cell atlas-like dataset from some published datasets to supplement some of our in-house data.

Are there best practices for integrating published single-cell data from different studies? For example should I start from raw fastq, or is there a possible shortcut using processed data objects (Andata, Seurat object, etc) #single_cell #scRNA #genomics

Happy to present this update to our (Jussi Taipale+me) plan to solve the cis-regulatory code using high-throughput assays of non-genomic DNA and ML, online today in Nature.
Despite the plan, the problem is so huge that we are looking to start a global effort in this space. Please email us if you want to join forces!
Thanks to all those who helped shape our thoughts!

https://rdcu.be/dtwyc

#HIV-infected cells hide in the brain and other tissues in people receiving antiretroviral therapy. Researchers might be able to use this knowledge to target these persistent viral reservoirs. #Microbiology https://elifesciences.org/digests/89837/hunting-hiv-holdouts?utm_source=mastodon&utm_medium=social&utm_campaign=organic

New Outlook is good, both for yourself and 766 third parties.

"The German government has launched a new Open Source software project called openDesk, which aims to reduce the country’s dependency on proprietary software vendors and support transparency and interoperability.

openDesk is a collection of Open Source software modules that are important for day-to-day work in the public sector, such as text creation, file collaboration, project management, email, calendar and messaging."https://opensource.net/governments-adopt-open-source-sovereignty/

I've switched from Chrome to Firefox about a decade ago. It's just as fast and intuitive, and container tabs are a game changer. It always catches me off guard when I see its market share is so low.

So tomorrow there are national elections in The Netherlands and I need to acquaint you with two oddities. For one, we take our democracy entirely for granted so we mostly vote in.. garbage bins. Secondly, our ballots are HUGE as they list 28 parties and 1128 candidates (no joke). So we need to make good use of the space in the garbage bin. For this purpose, polling stations are equipped with the STEMBUSSTAMPER, specially designed to tamp down wayward ballots:

I'm hoping for this appearance on the home page to give my door stopper designs a bit of publicity.

Unfortunately I can't add this model to the contest, and I wasn't given a heads-up that it would appear on the front page of Printables before it happened.

https://www.printables.com/model/79381-a-door-able-stop

#3DPrinting

Very interesting. Sequence-function relation is expected to be simpler than often expected, according to the preprint. I'd love to see comments or reviews on this one. #preprint #bioinformatics #protein

The simplicity of protein sequence-function relationships | bioRxiv
https://www.biorxiv.org/content/10.1101/2023.09.02.556057v1

I just found `alv` (https://github.com/arvestad/alv), a tool for viewing multiple sequence alignments on the command line, and it's perfect. I needed a tool to highlight differences and `alv -f fasta -t aa --only-variable aln.afa` does just that. Would prefer the numbering to start at 1 since sequence variants are 1-based #bioinformatics (Data from ERR031940.)

This is also a very common problem in academia

https://dannorth.net/2023/09/02/the-worst-programmer/

Speedrunners be like...
*A huge server with 72-core, with 7200% CPU usage.*
"What are you doing? Cracking ciphers? Mining data? Folding proteins? FEM simulation? Fuzzing 0day? Training neural nets?"
"Brute-forcing the game play of NetHack."

https://pellsson.github.io/ ​​

Two+ weeks 🚨 19/09/2023 15:00-17:15 BST 🚨until our 45th BSCB GenSoc UK Cilia Network e-symposium- free and open to all! >1260 folks already registered, this is the #cilia #centriole place to be! Not on my list already, sign up here: https://www.eventbrite.co.uk/e/bscb-gensoc-uk-cilia-network-e-symposia-series-tickets-122092125835

We have all good things lined-up: #GeneRegulatoryNetworks, #Signalling, mind-blowing #cryoET protein ID, #OrganelleProteomics in #neurons AND everything #tubulin! Join us...

#Artists cannot be replaced by some software. But it will take corporate execs a few years to learn it the hard way.

Meanwhile, artists will be hurting, bad. They will need our support — they always did!

So support them directly, if you can. Boost their toots on here, buy their merch, donate to them via whatever means they accept, or just send in a good word.

♦️♦️♦️

As this seems to be blowing up, a call to #art: this is now a "share your art" thread. I shall boost, if alt-text is provided. 💜

A new look at the architecture and dynamics of the Hydra nerve net. #ReviewedPreprint https://elifesciences.org/reviewed-preprints/87330?utm_source=mastodon&utm_medium=social&utm_campaign=organic

First post of my summer blog series on image communication in (bio/med) publications!

Today: Many papers, many images, many problems (and some first solutions).

Why we should make sure our figure are understandable.

https://helenajamborwrites.netlify.app/posts/image_numbers/

We've released v5.1.0 of our desktop bioinformatics platform! We've overhauled the installer for better support in Windows, made it easier to report problems to us and added new UI to show workflow progress. More info and download link on release note: https://labs.epi2me.io/epi2me-23.07-01-release/

Your first website is going to suck.
Your first blog post is going to suck.
Your first video is going to suck.
Your first app is going to suck.
...
.....
.
But if you keep trying 100 times, the 101st attempt will look like a work of Art.

TL;DR: Your first attempts may not be perfect, but keep trying. Perseverance is key.