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Posts by Kevin Bonham

As a recipient of federal grants from #NIH (for now! 😭) that funds research in my lab, I'd like to sincerely thank American taxpayers on #TaxDay for investing in scientific research that lays the foundation for medical and technological innovation in this country and keeps us ALL safe and healthy

3 days ago 447 125 7 11

I’m looking to hire a postdoc. We’re interested in the evolution of organs and cell types, and evolutionary and developmental genetics more broadly. Please reach out if you’re interested and please pass on to any folks that you know who might be! πŸͺ°πŸ§¬

5 days ago 7 8 0 0
Getting started | Species Distribution Toolkit Documentation for SpeciesDistributionToolkit.jl

In preparation for the next iteration of my data science class, I've made many updates to our #JuliaLang species distribution package. There's now a "Getting started" tutorial that, I think, is pretty good, and is meant to get you started within 20 minutes!

🌏

poisotlab.github.io/SpeciesDistr...

1 week ago 12 6 1 0
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As a decades long Linux supporter and user since the 90's, this is great. #cdnpoli
French πŸ‡«πŸ‡· President Macron πŸ”₯πŸ‘
"He plans to replace Microsoft Windows systems in French government with Linux to reduce reliance on πŸ‡ΊπŸ‡ΈU.S. tech and gain more control over its data."

1 week ago 196 57 8 6
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Episode 53 - Something catastrophic Can we use a single vaccine against chicken eggs to protect against literally every pathogen out there? Eh, probably not.

We covered this on a recent episode of @audiommunity.org ! It's neat immunology for sure, but I think calling it a "universal vaccine" is maybe a bit misleading. πŸ§ͺ

substack.com/@audiommunit...

1 week ago 3 1 0 0

You're welcome! I'm sorry for butchering the pronunciation of your name!

1 week ago 0 0 0 0

You are welcome here, strange visitor πŸ˜…

Apologies if I have the impression I was upset or irritated or something. I was only confused - I assumed someone that's been around long enough to remember Juno would know it was killed long ago.

1 week ago 1 0 1 0
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Would also be worth plotting this against federal tax revenue from those states. I know states like CA and MA pay a lot more in federal taxes than they pull in, but I'm not sure if that's because they pay more per capita, or because they have fewer people on things like medicade

1 week ago 1 0 0 0

We have always been at war with ~~Eastasia~~ Albania

1 week ago 2 0 0 0
GitHub - julia-vscode/LanguageServer.jl: An implementation of the Microsoft Language Server Protocol for the Julia language. An implementation of the Microsoft Language Server Protocol for the Julia language. - julia-vscode/LanguageServer.jl

github.com/julia-vscode...

And also github.com/JuliaEditorS... is a clearing house for other stuff. It would be really great to have another user-friendly option out from under the MS/GitHub boot heel

1 week ago 1 0 0 0

I personally am happy with nvim + julia-ls + slime + quarto-nvim.

It's a bit hacky to setup, though, and vs code is pretty nice out of the box for Julia use. Most of the active development is for vs code, but they do try hard to put as much as possible into generic things like LanguageServer.jl

1 week ago 0 0 1 0

The VS code extension does this very well - it launches a fully-featured REPL in the console. Actually, it's got even more than a normal REPL since there's some black magic that hooks into the editor so you can get in-line feedback from running the code.

1 week ago 1 0 1 0

Is 'now'? It's been more than 5 years I think since Seb stopped developing Juno and moved his efforts entirely to VSCode.

Great to see support for positron - more options for users is better, and to the extent that improvements can be upstreamed to the LS and generic editor support, all the better

1 week ago 1 0 1 0

On the latest episode of @audiommunity.org , @woodrufflab.bsky.social and I talk through this wonderful new paper.

A conceptually straightforward advance that massively expands the usefulness of this is kind of spatial 'omics πŸ§ͺ

1 week ago 10 2 0 1
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Freedom isn't free. It costs a buck oh five.

2 weeks ago 3 0 1 0

πŸ§ͺ

2 weeks ago 8 2 1 0

In a world where the US government is pulling back funding, this could be an especially great opportunity to be informed in some really cool science.

Not that private foundations can come anywhere close to making up the deficit, but still

2 weeks ago 1 0 0 0
Rankings of Julia books on Amazon

Julia is quickly becoming the successor to Fortran, once the standard for high-performance computing in science, mathematics, and engineering. It’s powerful and fun to use. Get a solid foundation with a good book:

lee-phillips.org/amazonJuliaB...

#julialang #physics #programming #mathematics

2 weeks ago 7 4 0 0

Alas, as with so many too-good-to-check stories, this one is BS πŸ§ͺ

www.scientificamerican.com/article/fact...

2 weeks ago 13 3 0 0

My main gripe with the alphafold example is how it shows you need decades and decades of high quality data, well structured, open and accessible to train a model -- and yet they always gloss over it and pretend it's just AI and magic. No, we need to continuously invest in real data and FAIR data.

2 weeks ago 216 85 4 5

Now I have 3 problems.

2 weeks ago 1 0 0 0
Lab tip: Set aside & save some buffer
Lab tip: Set aside & save some buffer YouTube video by the bumbling biochemist

Quick tip: Before you hook up your buffer to the FPLC, set aside some for needle washes, loop cleaning, spectrophotometer blanking, membrane washing, etc. And save some after for future uses like Bradford blanks, etc.
youtube.com/shorts/5-Cu2...

3 weeks ago 1 1 0 0
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Git for wetlab scientists - Git history conflicts How they happen, and what to do about them

History conflicts are one of the most annoying (and even scary!) things to deal with when you're learning git. But git is made for this! It's only annoying if you don't know what's going on.

Video 4 in a series about using #git for #wetlab scientists πŸ§ͺ

3 weeks ago 2 0 0 0

Really interesting integration of #julialang for the algorithms and #nextflow for the pipeline. In principal, the user doesn't need to know any julia to make use of this, but it lets the developers get all of the benefits of that language. Was a fun one too review, and happy to see it accepted!

πŸ§ͺ

3 weeks ago 1 0 0 0
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Video

Episode 3 of Under Review podcast is out!

The Hallucination in the Room - ChatGPT and fictional research

www.linkedin.com/pulse/halluc...

Spotify
open.spotify.com/episode/3NEX...

Apple
podcasts.apple.com/us/podcast/u...

YouTube
www.youtube.com/watch?v=g-Zt...

1/2

1 month ago 3 2 1 0
Almost none of the teenagers I chatted with admit to cheating with AI. When you ask teenagers about other students, however, you get a very different picture – 59% of teenagers told Pew that students at their school use AI to cheat while 34% said it happens extremely or very often.
"I've had classmates who like literally yell at the teacher, 'Hey, if you don't come answer my question, I'm just gonna get AI to do this for me'," Rieban says. Cash, his 14-year-old brother, has similar stories. "In science class, we had to research a topic and write about it and one of the kids at my table had just completely copied what the AI told him," he says. "But then he couldn't read his own handwriting and he didn't even remember what he wrote."

Almost none of the teenagers I chatted with admit to cheating with AI. When you ask teenagers about other students, however, you get a very different picture – 59% of teenagers told Pew that students at their school use AI to cheat while 34% said it happens extremely or very often. "I've had classmates who like literally yell at the teacher, 'Hey, if you don't come answer my question, I'm just gonna get AI to do this for me'," Rieban says. Cash, his 14-year-old brother, has similar stories. "In science class, we had to research a topic and write about it and one of the kids at my table had just completely copied what the AI told him," he says. "But then he couldn't read his own handwriting and he didn't even remember what he wrote."

β€˜59% of teenagers told Pew that students use AI to cheat, while 34% said it happens extremely or very often.’

God help this generation.
We have allowed Big Tech to convince us that β€˜AI is revolutionizing the world’ and we’re sacrificing the development and well being of children to their Mammon.

4 weeks ago 400 122 16 23

I am reviewing a simply amazing paper from a relatively young US-based lab, which is in danger of shutting its doors later this year. My emotions are all over the place.

The fact that this does not uniquely identify the lab I’m referring to just deepens the tragedy of this moment in US science.

4 weeks ago 369 71 5 4
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An Immense World (Young Readers Edition): How Animals Sense Earth's Amazing Secrets How Animals Sense Earth's Amazing Secrets

My 7 year old, while reading the adapted-for-kids version of "An Immense World" - "Do you really think one person could write this whole book? Where does @edyong209.bsky.social get all of his ideas from?!?"

I told him I would ask πŸ˜‰

bookshop.org/p/books/an-i...

1 month ago 6 2 0 0
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Join #MVIF 47 cassyni.com/s/mvif-47
and #MeetTheSpeakers

We are delighted to welcome Lindsay Hall (@halllab.bsky.social‬) as a keynote speaker, who will discuss early life microbiome dynamics!

1 month ago 1 3 1 0
Rankings of Julia books on Amazon

Need your #code to be faster but don’t want to use Fortran or C? Learn #Julia, the modern language for #HPC, with a quality book. Here are some options:

lee-phillips.org/amazonJuliaB...

#julialang - its speed and friendly syntax is taking it beyond #science to #finance and other areas.

1 month ago 3 3 1 0