Andrew Kennard @askennard@qoto.org

I'm trying to classify ~500 proteins into groups. NOT using Gene Ontology (GO) terms. PANTHER protein classification works well, but ~20% have no classification.

Does anyone have suggestions for alternative ways to do this?

#Bioinformatics #BioinformaticsHelp #CellBiology

Finally made an #ImageJ macro to generate rotated zoom boxes!

Now that's an eye-catching title!

🔬First Mastodon post alert!☺️
Hey there, I'm Delnia, and I've just embarked on my PhD journey in Cellular and Structural Biology at IGBMC, University of Strasbourg.🧬
I'll be focusing on unraveling the (ultra)structural mysteries of Golgi organization under the expert guidance of Florian Fabler. 🧪🔍
A repost would be fantastic as I'm building my network here on Mastodon.
Let's connect and explore the world of science together!
#phdlife #CellBio #cryoET #IGBMC #structurebiology #introduction

A wow prescient quote from 1865 that will resonate with my anti-reductionist friends

“Physiologist and physicians must never forget that a living being is an organism with its own individuality. Since physicists and chemists cannot take their stand outside the universe, they study bodies and phenomena in themselves and separately, without necessarily having to connect them with nature as whole. But physiologists, finding themselves, on the contrary, outside the animal organism which they see as a whole, must take account of the harmony of the whole, even while trying to get inside, so as to understand the mechanism of its every part. The result is that physicists and chemists can reject all idea of the final causes for the facts that they observe; while physiologists are inclined to acknowledge a harmonious and pre-established unity in an organized body, all of whose partial actions are interdependent and mutually generative. We really must learn, then, that if we break up a living organism by isolating its different parts, it is only for the sake of ease in experimental analysis, and by no means in order to conceive them separately. Indeed, when we wish to ascribe to a physiological quality its value and true significance, we must always refer to this whole, and draw conclusions only to its effects in the whole.”

Stumbled upon via this excellent take about homestasis (and how it's anti-reductionistic)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7076167/pdf/fphys-11-00200.pdf

Claude Bernard, 1865

We love thinking about how our science + society coverage can better inform, engage, and empower you. That's why we are partnering with the Solutions Journalism Network to pilot the What’s Working Factbox.

Embedded within our stories, the window connects you with articles from the Solutions Story Tracker® produced by us and our friends like Next City, Yes! Magazine, and the Christian Science Monitor.

Learn more here: https://www.solutionsjournalism.org/organizations/factbox

#science #news #innovation #journalism

collaboration with jn3008

Interested in how cells influence their neighbours?

Want a flexible, sensitive, unbiased approach to explore neighbour responses?

Tamina Lebek presents PUFFFIN: Positive Ultra-bright Fluorescent Fusion For Identifying Neighbours

PUFFFIN has SO MANY great features and we are very excited about using it to understand development, homeostasis, and disease

Here are some of the clever tricks that Tamina thought up to make this system so useful...

1/n

https://www.biorxiv.org/content/10.1101/2023.09.06.556381v1

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.)

“In a way, the people our cars mow down are doing just as much as our highly paid programmers and engineers to create the utopian, safe streets of tomorrow. Each person who falls under our front bumper teaches us something valuable about how humans act in the real world.” #AI https://www.mcsweeneys.net/articles/our-self-driving-cars-will-save-countless-lives-but-they-will-kill-some-of-you-first?utm_source=werd.io&utm_campaign=mastodon&utm_channel=mastodon

Job ad for a colleague:

Postdoc on microscopy at the Bioengineering in Reproductive Health Research Group in Barcelona.

Open position for a postdoc with a background in optics and/or microscopy, to study human oocytes using hyperspectral imaging at #IBECBarcelona

https://ibecbarcelona.eu/es/postdoc-on-microscopy-at-the-bioengineering-in-reproductive-health-research-group/

#Barcelona #DevBio

Are there any microscopists hiding here?
Adding :AddBiophysicist to this post in order to get in the "Biophysicists on Mastodon" list...

#Biophysics #Microscopy #SMLM

a Portrait of Tenochtitlan, my 3D reconstruction of the capital of the Aztec Empire is released!

I've been looking forward to this for a long time, and I am really curious what all of you think.

Take a look:
http://tenochtitlan.thomaskole.nl

#tenochtitlan

I see a lot of people sharing blanket condemnations of all of those who still remain on #Twitter / #Xitter , and I need you to slow down a bit.

Sure, in some cases this is justified - journalists should really know better. But there are a lot of communities on that platform that are vital to many people's well-being that _haven't_ been replicated on the #Fediverse or elsewhere. Take #BlackTwitter - while #BlackMastodon is growing, it's still minuscule in comparison. The number of Twitter users in #Pakistan is staggering, while they are only a handful on #Mastodon . And so on, and so forth. Twitter was a lifeline to many marginalized people, and it still is - even though it gets worse every day - and we need to recognize this.

As a white European guy, it was easy for me to walk away from Twitter (I still have an account there, but I only post "you should go to Mastodon" stuff these days) - since it is easy to find people of a similar background to interact with. But this is NOT true for everyone!

So I'd like everyone to show a bit less contempt to the remaining Twitter users in general, and put some more effort in how to make the Fediverse friendlier to marginalized voices. Because there is MUCH work to be done here!

This is one of the most incredible pieces of research into a random piece of infrastructure I’ve ever seen. A wild ride.

https://tylervigen.com/the-mystery-of-the-bloomfield-bridge

h/t @danyork

🔬First method-focused work from our lab is just out in Cell Reports Methods 🎉
Interested in multicolor SMLM? Check the open-access final version of Karoline Friedl's PhD work, with Sandrine Lévêque-Fort's lab and the Abbelight gang
https://www.cell.com/cell-reports-methods/fulltext/S2667-2375(23)00215-1

Nothing destroys a graduate career faster than help avoidance.

For all the folks starting their #PhD (or their master thesis) today - a reminder why your PhD advisor can solve a problem so "easily" ...

#astrodon #academia #AcademiChatter #research

New @biorxivpreprint manuscript from my lab that sheds light on part of the dark genome, unannotated or poorly annotated genes in the genome. In it, we show that the highly conserved HEATR5 protein is a component of two biochemically distinct protein complexes.

https://www.biorxiv.org/content/10.1101/2023.08.24.554671v2