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Jim Rybarski

@jimrybarski

Boston-area computational biologist Blog: https://www.rybarski.com

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14.04.2024
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Latest posts by Jim Rybarski @jimrybarski

Search engines are such a central tool and I can’t overstate how nice it is to have one that doesn’t actively try to exploit you with every use. Highly recommend Kagi

27.02.2026 16:50 👍 1 🔁 0 💬 0 📌 0

These are concentration camps and its our duty as citizens to ensure these things don't get built.

14.02.2026 00:28 👍 5250 🔁 2044 💬 59 📌 19
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This is literally what CURRENT LAW requires. It’s in the Constitution! www.politico.com/news/2026/02...

10.02.2026 03:18 👍 11250 🔁 3121 💬 237 📌 232
A terminal session where I ssh into a server and receive this warning: WARNING: connection is not using a post-quantum key exchange algorithm. This session may be vulnerable to "store now, decrypt later" attacks. The server may need to be upgraded. See https://openssh.com/pq.html

A terminal session where I ssh into a server and receive this warning: WARNING: connection is not using a post-quantum key exchange algorithm. This session may be vulnerable to "store now, decrypt later" attacks. The server may need to be upgraded. See https://openssh.com/pq.html

what fresh hell is this

01.02.2026 16:47 👍 2 🔁 0 💬 0 📌 0

i think this MLK day the thing to focus on is the strategic focus and tactical brilliance of the civil rights movement and the way it was laser focused on a set of achievable goals

19.01.2026 15:05 👍 17484 🔁 3416 💬 201 📌 151

Spam

10.01.2026 04:35 👍 0 🔁 0 💬 0 📌 0

It’s 2026, still no Armata, but cutting edge warfare brought a horse with Starlink instead

08.01.2026 07:26 👍 419 🔁 60 💬 13 📌 10
This is a screenshot of a Craigslist ad. It reads: "I need help developing a comprehensive map of all possible surgeries that can be performed on the human body.

I can offer a competitive salary, and I am looking to hire someone with an open mind, as well as experience in the surgical reattachment of limbs and body parts, and the surgical integration of new tissue from external sources.

Thank you for your time, and I look forward to hearing from you."

This is a screenshot of a Craigslist ad. It reads: "I need help developing a comprehensive map of all possible surgeries that can be performed on the human body. I can offer a competitive salary, and I am looking to hire someone with an open mind, as well as experience in the surgical reattachment of limbs and body parts, and the surgical integration of new tissue from external sources. Thank you for your time, and I look forward to hearing from you."

Definitely not making a Frankenstein

30.12.2025 19:17 👍 1 🔁 0 💬 0 📌 0

PSA for people with NIH grant periods starting January 1st (including most NIGMS MIRAs): your RPPR is due Saturday, but they haven’t sent out the usual automated reminders, presumably due to the shutdown

11.11.2025 01:20 👍 93 🔁 83 💬 0 📌 3
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Nature suggests you use their "Manuscript Adviser" bot to get advice before submitting

I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:

03.11.2025 13:55 👍 873 🔁 252 💬 35 📌 28
Hundreds of thousands of people convene at the Boston Commons for the No Kings protest on a sunny cool day. John Hancock’s signature is visible at the top of a building in the distance.

Hundreds of thousands of people convene at the Boston Commons for the No Kings protest on a sunny cool day. John Hancock’s signature is visible at the top of a building in the distance.

18.10.2025 18:07 👍 2 🔁 0 💬 0 📌 0
Did people really memorize phone numbers before cell phones, or is that just a movie thing?
2? Questions
I was watching some old shows from the 90s and noticed people would just dial numbers from memory - like they'd call their friends or family without looking anything up.
Made me wonder if that was actually normal back then? Did people genuinely have all their important numbers memorized, or did most folks keep a little address book or written list nearby?

Did people really memorize phone numbers before cell phones, or is that just a movie thing? 2? Questions I was watching some old shows from the 90s and noticed people would just dial numbers from memory - like they'd call their friends or family without looking anything up. Made me wonder if that was actually normal back then? Did people genuinely have all their important numbers memorized, or did most folks keep a little address book or written list nearby?

If anyone needs me I will be in the museum, lying down next to the bog bodies.

13.10.2025 17:58 👍 23795 🔁 4865 💬 1519 📌 1782

Odd to consider, but T-Rex had a Krebs cycle

11.10.2025 17:16 👍 26 🔁 3 💬 0 📌 0

As I tell my students, if you arrived at a simple answer in biology you have done one of two things: arrived at the wrong answer or asked the wrong question

09.10.2025 14:38 👍 49 🔁 18 💬 4 📌 1
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We still can’t predict much of anything in biology Biology is hard. Yes, even for AI.

Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...

07.10.2025 16:11 👍 173 🔁 68 💬 5 📌 6
Preview
GPU-accelerated homology search with MMseqs2 - Nature Methods Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com

21.09.2025 08:06 👍 174 🔁 63 💬 4 📌 2

Related frustration: co-authorship is rarely on the publisher’s website and can usually only be determined by downloading the pdf

20.09.2025 21:03 👍 2 🔁 0 💬 1 📌 0
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New blog post – A quick look at Roche's SBX
lh3.github.io/2025/09/11/a...

12.09.2025 03:26 👍 57 🔁 30 💬 2 📌 3

"PhD-level experts in your back pocket" is a completely nonsensical description of AI but a pretty good description of social media if you follow the right people

09.08.2025 23:07 👍 10431 🔁 2012 💬 136 📌 170
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Read out all of the text on your slides I have a simple rule for better public speaking: If you’re using slides that contain text, you must read it out, word-for-word.

A simple rule for better public speaking: If you’re using slides that contain text, you must read it out, word-for-word.

clauswilke.substack.com/p/read-out-a...

20.07.2025 15:58 👍 36 🔁 12 💬 4 📌 2
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Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco

07.07.2025 08:21 👍 153 🔁 70 💬 8 📌 3
A picture of a bottle of hummus. It is labeled NATURE HUMMUS

A picture of a bottle of hummus. It is labeled NATURE HUMMUS

These NPG spinoff journals are out of control

29.06.2025 16:50 👍 479 🔁 70 💬 12 📌 7

Correct. People who say otherwise either don't understand the numbers, or are engaging in wishful thinking.

04.06.2025 01:41 👍 130 🔁 25 💬 7 📌 0

It's really important that what's happening at Harvard is not covered just as research cuts but as an all-out assault on higher education. This administration has explicitly said their goal is to destroy, or at the very least dramatically reshape, these institutions.

16.05.2025 21:05 👍 173 🔁 42 💬 5 📌 2
A screenshot of the termination notice showing "Outstanding Investigator Grants"

A screenshot of the termination notice showing "Outstanding Investigator Grants"

A screenshot of the termination notice with "This award is terminated effective the date of this award, due to unsafe antisemitic actions that suggest the institution lacks concern for the safety and wellbeing of Jewish students." highlighted

A screenshot of the termination notice with "This award is terminated effective the date of this award, due to unsafe antisemitic actions that suggest the institution lacks concern for the safety and wellbeing of Jewish students." highlighted

Yesterday, the NIH R35 “Outstanding Investigator” grant to fund scientists in my lab studying antibiotic resistance was terminated for reasons not related to the content of the science, or any actions taken by me or members of my lab

13.05.2025 23:37 👍 879 🔁 579 💬 144 📌 73

I can't recommend Kagi enough - it isn't free, but in return you get a search engine that isn't trying to exploit you. More importantly though, I find the results much better than Google's.

11.05.2025 18:03 👍 7 🔁 0 💬 0 📌 0

Absolutely not an exaggeration. High crimes and misdemeanors committed and endorsed in the Oval Office on live television.

14.04.2025 16:18 👍 2364 🔁 642 💬 26 📌 17

Hi. I’m an expert in modernizing legacy government software systems. This is profoundly stupid and will definitely fail, and it’s just a question of whether our social security system fails along with it.

28.03.2025 14:54 👍 4144 🔁 1589 💬 214 📌 89

They are just disappearing people off the street. Having a hard time thinking about literally anything else.

27.03.2025 05:15 👍 27183 🔁 8995 💬 1865 📌 794
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75% of US scientists who answered Nature poll consider leaving More than 1,600 readers answered our poll; many said they were looking for jobs in Europe and Canada.

We polled Nature readers to ask if they were thinking of leaving the US for jobs abroad. Three-quarters of them (who said they were US-based scientists) said yes. 🧪

www.nature.com/articles/d41...

27.03.2025 14:19 👍 2332 🔁 1067 💬 65 📌 216