iiinova — where your digital self keeps evolving

Ben Neely @benneely.com · 25/09/2026

One of my fav TOC graphics for sure, and answers the age old question: where Do Proteomics People Come from? From @proteomicsnews.bsky.social using our guests on #THEProteomicsShow plus surveys. Good to share with the kids, but also read yourselves. pubs.acs.org/jamsef/artic...

221

Ben Neely @benneely.com · 23/09/2026

I know AI is the end of the world, but oh it makes me smile.

030

Ben Neely @benneely.com · 21/09/2026

Well Ben @proteomicsnews.bsky.social and I are trying to be podcasters again and continuing the @us-hupo.org All the Parts #THEProteomicsShow series. To give you a behind the scenes look, I wrote 8 emails this morning either bugging people or cold calling. BUT, we *are* starting to record (Friday!).

052

Ben Neely @benneely.com · 02/09/2026

Got to see Laura Herring IRL today, in Chucktown! No offense to other peeps at Waters but she’s my fav Waters person now.

141

Ben Neely @benneely.com · 27/08/2026

I haven’t worked at MUSC for 10 years, yet my name is still in front of my old building. But I am in good company. Just glancing I know Tom and Adam (at least) retired and Jennifer is now at Florida (you’ll remember her and snot from #THEProteomicsShow).

110

Ben Neely @benneely.com · 25/08/2026

Not science: you can guess what we’re watching tonight. (And searching with this movie’s title does NOT give the results I wanted)

020

Ben Neely @benneely.com · 20/08/2026

For you PDV and Sage (via @michaellazear.bsky.social) proteomic analysis lovers out there, they now work together in the latest PDV version: github.com/wenbostar/PD... Big thanks to Bo Zhang for getting to this so quick.

240

Ben Neely @benneely.com · 18/08/2026

Not science: just finished Ursula Le Guin’s Rocannon’s World (audiobook) and though the narrator grated me at the start, my gods her prose is gorgeous, efficient, and elegant all at once.

170

Ben Neely @benneely.com · 13/08/2026

As a huge fan of Joe versus the Volcano and spend a lot of time with Claude Code these days (we are evaluating things at work)… and everytime I see this line I can’t help but think of Meg Ryan.

000

Ben Neely @benneely.com · 23/07/2026

Trigger warning, DNA! I bought this shirt to wear at proteomics things. Could be fun to get the DC RF shirt too that I think I saw @lindsaykpino.com with. And yes, woot shirt is running a buy 2 get 2 deal.

140

Ben Neely @benneely.com · 21/07/2026

So if you ask an LLM to make a list of p-values to identify differentially abundant proteins, can we make it say "I cannot write the function as requested because it would violate a Hard Constraint from the proteomics grounding specification (ie, multiple testing correction is not optional)." 3/7

130

Ben Neely @benneely.com · 21/07/2026

If context management isn't on your radar yet, it should be. Ex. I made a repo template just for my own workflow context management. But the idea here was to use context management to help make vibe-coded software not break rules set in the GROUNDING.md. github.com/neely/agent-... 2/7

211

Ben Neely @benneely.com · 14/07/2026

I really thought it was called shaggin on the pier but now the internet says I’m crazy. Found this on the fb for some history.

010

Ben Neely @benneely.com · 09/07/2026

I saw this heatmap (a literal one) posted by @inrng.com and it looks legit!

110

Ben Neely @benneely.com · 09/07/2026

Not science: I think the thing people may not appreciate about certain heat, isn’t how hot it is during the day, but the fact it never cools off. Thank the tiny gods for AC at night. Also, it being hot in places that aren’t used to heat or don’t have AC (or southern France and Le Tour)… ugh.

130

Ben Neely @benneely.com · 08/07/2026

AI trigger warning What I’ve learned so far: 1) scope creep is really hard to fight 2) PTM Shepherd was clever 3) there isn’t an obvious exhaustive ptm dataset to validate on, more of a DIY or algo competition approach for vetting 4) I like Cline 5) I have other things I’m supposed to be working on

050

Ben Neely @benneely.com · 06/07/2026

Even the end! Santi, who already missed most of last season at Milan for ankle surgery, rolls his ankle super bad, making them man down on the corner and arguably handicapping what could have been an equalizer. I thought the US v B-H ending was tense. This game was epic.

000

Ben Neely @benneely.com · 05/07/2026

Took me a while to realize our local 250th events were somewhat unique… we’re a signature city! Fun part is that meant we had some new extra big fireworks in the harbor tonight. americasnationalparks.org/americas-250...

100

Ben Neely @benneely.com · 01/07/2026

In other words, all of this is just me in chat on my phone (this isn’t new or elegant but I hadn’t tried this setup). Ex. Can’t sleep, make some changes, all gets pushed.

000

Ben Neely @benneely.com · 26/06/2026

Not science: do other regions/countries do a tomato sandwich? Pretty classic go-to this time of year in the southeast. (Other tomato things too like tomato pie and okra and tomatoes become pervasive now.)

200

Ben Neely @benneely.com · 23/06/2026

GenAI really is great for those of us with foundational knowledge. But this future of those without that knowledge being genAI enabled is likely fast approaching. It is satire (right? … RIGHT???), but this is like when the onion is too close to reality.

480

Ben Neely @benneely.com · 12/06/2026

For this week’s #THEProteomicsShow, me and Ben @proteomicsnews.bsky.social had the great pleasure of having Keith Baar @musclescience.bsky.social on to chat muscles and tendons. I know I keep saying it, but this was my fav. Find it wherever you find fine podcasts or here anchor.fm/theproteomic...

130

Ben Neely @benneely.com · 11/06/2026

This is Encino Man btw which is all I can hear in my head while this silliness continues.

000

Ben Neely @benneely.com · 11/06/2026

Not science: I didn’t realize the orange ball people did puns so well. Knickelback, Knickole Kidman, and Stevie Knicks… thanks to Tay Tay et al. (Been watching finals so I can converse with Ben @proteomicsnews.bsky.social)

200

Ben Neely @benneely.com · 09/06/2026

can I do that?!!!! later: I can! obviously the excellent cursor is on desktop, and do a ctrl+shit+r to refresh cache to see it (spoiler: it has a trail!)

110

Ben Neely @benneely.com · 09/06/2026

I love how ugly it is!

100

Ben Neely @benneely.com · 05/06/2026

This week’s #THEProteomicsShow with me and Ben @proteomicsnews.bsky.social is all about skin. We had the marvelous Dr. Beatrice Dyring-Andersen of Skin Atlas fame (skin.science/about) discuss the most beautiful organ. Get it wherever you find fine podcasts or anchor.fm/theproteomic...

020

Ben Neely @benneely.com · 29/05/2026

Here it is if you don't want to click.

000

Ben Neely @benneely.com · 29/05/2026

I get to do 1 random thing per #THEProteomicsShow season, so talking to Laura Thompson about blow (aka beluga exhaled breath condensate) seemed perfect. Ben @proteomicsnews.bsky.social went in blind, and it turned out to be pretty freaking awesome. Find it wherever or here anchor.fm/theproteomic...

101

Ben Neely @benneely.com · 25/05/2026

👀 What, there was a new #THEProteomicsShow with Ben @proteomicsnews.bsky.social and me?! We continue our march down the body, this week with Kevin Schey talking about eyeballs and proteomics. Find it wherever you find fine podcasts or here anchor.fm/theproteomic...

200

Ben Neely @benneely.com · 15/05/2026

This week on #THEProteomicsShow, Ben @proteomicsnews.bsky.social and I finally get to sit down with @jochwenk.bsky.social and talk blood (this has been on my wish list for a while, and didn't disappoint). Find it wherever you find fine podcasts or here: anchor.fm/theproteomic...

260

Ben Neely @benneely.com · 15/05/2026

We have chamber of commerce weather today with brisk temps, lowish humidity, and not a cloud in the sky. I have already encouraged 2 people to take leave and bug out, and might even do so myself.

000

Ben Neely @benneely.com · 14/05/2026

It got picked up by my weekly proteomics horizon scanner (1 of 5, I limit at 5). B-)

111

Ben Neely @benneely.com · 08/05/2026

Did you always want to know more about snot and all the things it can tell you? Well do I have a show for you! This week's #THEProteomicShow me and Ben @proteomicsnews.bsky.social sit down with Jennifer Mulligan to talk snot. Find it wherever you find fine podcasts or anchor.fm/theproteomic...

023

Ben Neely @benneely.com · 03/05/2026

And in case it wasn’t clear, this paper wasn’t promoting vibe coding everything but more accepting the coming reality and asking “how can we make it suck less”. The idea that everything will be JIT bespoke vibe coded is wild/empowering/terrifying.

Source is https://www.ijustvibecodedthis.com

210

Ben Neely @benneely.com · 01/05/2026

This is a funny picture for them to use (and I should read it first), but last year the wet spring laid ruin to most of the strawberries as fungus was spreading by wind all over. This year the dryness has led to a bumper crop for strawberries at least, largely because of lack of disease.

Taken last weekend at Ambrose on Wadmalaw.

000

Ben Neely @benneely.com · 01/05/2026

All the Parts continues on #THEProteomicsShow, this week with Charlie Schurman talking to me and Ben @proteomicsnews.bsky.social about bones (not Star Trek). No joke, learned way more than I expected. Find it wherever you find fine podcasts or here anchor.fm/theproteomic...

342

Ben Neely @benneely.com · 30/04/2026

So today is the first legit rain we’ve gotten in maybe 2 months, and so we have running jokes about how we’ve all forgot what to call this moisture falling from the clouds. My vote is sky water. It might even continue sky watering for a couple days! 🤯

110

Ben Neely @benneely.com · 24/04/2026

Almost forgot, you can find the latest episode of #THEProteomicsShow out today as we continue our biological voyage. This week me and Ben @proteomicsnews.bsky.social talked to Lekha Sleno about tears. No crying it was awesome. Find it wherever you find fine podcast or here anchor.fm/theproteomic...

012

Ben Neely @benneely.com · 24/04/2026

Is there a way to help non-coder proteomics pros, AI-pros who don't know proteomics, or total novices vibe code proteomics software with confidence? Maybe. We are proposing a epistemic grounding context file, but there is still a ton left to do: arxiv.org/abs/2604.21744 @magnuspalmblad.bsky.social

AI generated graphic making a reference to the Drake meme.

381

Ben Neely @benneely.com · 17/04/2026

Back from 🌄Spring Break🏖️, a new episode of #THEProteomicsShow is out. Ben @proteomicsnews.bsky.social and I sat down with Drs. Sasha Singh @toleafgirl.bsky.social and Sarah Parker to chat all things blood vessels. Find it wherever you find fine podcasts, or here anchor.fm/theproteomic....

031

Ben Neely @benneely.com · 14/04/2026

A [not actually in a] movie couple that would definitely have a podcast. #THEProteomicsShow

170

Ben Neely @benneely.com · 13/04/2026

There are tons of ELI5 explanations for LLMs, but this one from @quantamagazine.bsky.social seemed especially apt. "Chatbots are “yes, and” improv machines designed to spit out strings of words that sound plausible because they’re statistically likely." The parallels with this movie are spot on.

110

Ben Neely @benneely.com · 10/04/2026

Kinda science: on vacation at Airbnb in Valle Crucis, owned by Parley Rasmussen [a biochemist in the Standards Division, Department of Agriculture (from obit)], who gifted 500 acres to state for park. When sold house in ‘22 they left some of his old stuff. But haven’t found his publications yet. 🤷‍♂️

120

Ben Neely @benneely.com · 08/04/2026

I can’t tell if this amalgamation is the best thing ever and pure brilliance, or just super weird. But if you’re ever in the south side of Soda City, this exit has it all.

110

Ben Neely @benneely.com · 07/04/2026

MS proteomics skywalkers... can I again iterate that we might have a problem. This 👇 is "proteomics space".

330

Ben Neely @benneely.com · 02/04/2026

Did I see hear we are in one of the longest spring droughts, at least on JI?

000

Ben Neely @benneely.com · 02/04/2026

All the Parts continues on #THEProteomicsShow as me and Ben @proteomicsnews.bsky.social ask pretty dumb questions about stuff. Today is Jan Mulder chatting brain, and it was awesome talking about all things brains. Find it wherever you find fine podcasts, or here anchor.fm/theproteomic...

141