@p_maverick_b Plan on higher journal fees. You don't want to publish in a low-class journal ;-)
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Tom Knight -- e/๐ฆ๐ด
1.2K posts
Tom Knight -- e/๐ฆ๐ด
@TomKnightSynBio
Engineer of stuff that is alive or computes. Follow us all to that blue place.
๊ฐ์
์ผ Ocak 2021
3.7K ํ๋ก์3K ํ๋ก์
Reagents $200
Cloud $150
Rent $800
Journal fees $3,600
Utility $150
someone who is good at the economy please help me budget this. my lab is dying
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@SynBio1 Please forward all such notifications to my agent for handling.
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My new startup is an AI agent that tracks your physical state and if you're not well it sends you relentless and unblockable notifications telling you to stop and rest
Basically we're reinventing pain from first principles
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Tom Knight -- e/๐ฆ๐ด ๋ฆฌํธ์ํจ
First in Human! When @rhomsany and I first started Octant, this was the dream. A platform that makes molecules that few others can go afterโฆ to get the chance to tackle severe diseases with poor to no standard of care. It's been a long journey but so incredibly proud of the team and thankful to the volunteers who make this attempt possible. We got to celebrate with these new sunhats! octant.bio/news/octant-anโฆ
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@ATinyGreenCell Instructive, but I think you missed the opportunity to tell people the *purpose* of these reagents. Cookbooks don't yield understanding, which you need to update and improvise when things change.
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I used the extracted gDNA from tonight's prep to try and PCR a larger chunk of petunia genome hunting for one of its ubiquitin genes. I'm using a published genome as reference but its not my cultivar so need to go fishin. Detection primers worked (UBQ10 conserved) but others iffy
Sebastian S. Cocioba๐ช๐ท@ATinyGreenCell
Let's extract some DNA from a petunia leaf together! ๐งฌ๐งต 1/n
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Tom Knight -- e/๐ฆ๐ด ๋ฆฌํธ์ํจ
์์์ ๋ณด๊ณ ๋๋, Ginkgo RAC์ ํด์๋ ํ๋์จ์ด ๋ํผ(hardware wrapper), ์ํํธ์จ์ด ๋ํผ(software wrapper)๋ค์.
๊ธฐ์กด์ ๋ฐ์ด์ค ์ฅ๋น ์์ฅ์ Thermo Fisher, Agilent, Danaher ๋ฑ ๊ฐ ๋ฒค๋๊ฐ ์์ ๋ค๋ง์ ํ์์ ์ธ ๊ท๊ฒฉ๊ณผ ์ํํธ์จ์ด๋ฅผ ๊ณ ์งํ์ฌ ํธํ์ฑ์ด ๋จ์ด์ง๋ ํํธํ๋ ์์ฅ์ด์์ต๋๋ค.
Ginkgo๋ ์ด์ง์ ์ธ ํ์ฌ ์ฅ๋น๋ค์ ์์ ๋ค์ '๋ํผ(Wrapper)'๋ก ๊ฐ์ธ์ ์๋ฒฝํ๊ฒ ํตํฉ๋ ํ๋์ ์์คํ
์ผ๋ก ํ๋ฐ๊ฟ์์ผ๋ฒ๋ฆฝ๋๋ค.
1. ํ๋์จ์ด ๋ํผ (Hardware Wrapper): ํํธํ๋ ์ฅ๋น์ '๋ ๊ณ ๋ธ๋กํ'
RAC์ ์ผ์ข
์ 'ํ์คํ๋ ๊ป์ง(Standardized wrapper / envelope)โ์
๋๋ค.
- ๋ฌผ๋ฆฌ์ ์ธํฐํ์ด์ค์ ํต์ผ: ์์ค์ ํ๋งค๋๋ ์์ฌ๋ถ๋ฆฌ๊ธฐ, ๋ฐฐ์๊ธฐ, ์ก์ฒด ๋ถ๋ฐฐ๊ธฐ ๋ฑ์ ํฌ๊ธฐ์ ๋ชจ์์ด ๋ชจ๋ ๋ค๋ฆ
๋๋ค. Ginkgo๋ ์ด ๊ฐ๋ณ ์ฅ๋น๋ค์ 6์ถ ๋ก๋ด ํ๊ณผ ์๊ฐ๋ถ์ ์ํ ์ด์ก ํธ๋(Magnumotion track)์ด ์ฅ์ฐฉ๋ ํ์คํ๋ ์นดํธ(RAC) ์์ ์ง์ด๋ฃ๊ณ ๊ฐ์ธ๋ฒ๋ฆฝ๋๋ค.
- ๋ณต์ ๋ฐ ํ์ฅ์ฑ์ ํด์: ํน์ ์ฅ๋น(์: ํ๋ ์ดํธ ์ค๋ฌ)๋ฅผ RAC์ ๋ง๊ฒ ํตํฉํ๋ ์ด๊ธฐ ์ค๊ณ(ํ๋ ์ ๋ฐ ์ต์ปค ํฌ์ธํธ ๊ฐ๋ฐ)๋ฅผ ํ ๋ฒ ์๋ฃํ๊ณ ๋๋ฉด, ์ดํ๋ถํฐ๋ ์ถ๊ฐ R&D ์์ด ๊ทธ์ โ๋ณต๋ถ(copy and paste)" ํ๋ฏ ์ฐ์ด๋ด์ด ๋น์ฉ๊ณผ ์๊ฐ์ ํ๊ธฐ์ ์ผ๋ก ์ค์ผ ์ ์์ต๋๋ค. ์ด๋ก ์ธํด์ ๊ณ ๊ฐ์ด ์ํ๋ฉด ์ธ์ ๋ ์๋ก์ด ๊ธฐ๋ฅ์ ๋ ๊ณ ๋ธ๋ก์ฒ๋ผ ์ฝ๊ฒ ์ถ๊ฐํ ์ ์์ต๋๋ค.
2. ์ํํธ์จ์ด ๋ํผ (Software Wrapper): '๋์ฐํ(Heinous)' ๋ฒค๋ ์ํํธ์จ์ด์ ์ถ์ํ
ํ๋์จ์ด ํตํฉ๋ณด๋ค ํจ์ฌ ๋ ๊ฐ๋ ฅํ ํด์๋ ๋ฐ๋ก ์ํํธ์จ์ด ๋จ์์ ๋ฐ์ํฉ๋๋ค.
- ํ์์ ์ธ ๋ฒค๋ API์ ๊ทน๋ณต: ๋ง์ ์ฅ๋น ๋ฒค๋๋ค์ ํ์ฌ์ ํตํฉ์ ๋ง๊ณ ์์ฌ ์ํํธ์จ์ด๋ง ์ฐ๊ฒ ํ๋ ค๊ณ ์๋์ ์ผ๋ก API๋ฅผ ์ ๊ณตํ์ง ์๊ฑฐ๋ ํ์์ ์ผ๋ก ์ด์ฉํฉ๋๋ค. Ginkgo๋ ๊ณ ๊ฐ์ด ์์ฒญํ๋ ์ฅ๋น๋ฅผ ์์คํ
์ ์ฌ๋ฆฌ๊ธฐ ์ํด ์ง์ ๋๋ผ์ด๋ฒ๋ฅผ ๊ฐ๋ฐํ๊ฑฐ๋ ์ฅ๋น์ ํ๋์์ด์ด๋ง(Hardwire)ํ๋ ๊ณ ๋ ์์
์ ์ํํฉ๋๋ค. ์ฅ๋น ํ๋๋ฅผ ํตํฉํ๋ ๋ฐ 1~2๊ฐ์์ด ๊ฑธ๋ฆฌ๋ ํ๋ ๊ณผ์ ์ด์ง๋ง, ํ ๋ฒ ํตํฉํด ๋์ผ๋ฉด ์๊ตฌ์ ์ผ๋ก ์์คํ
์์ ์ฌ์ฉํ ์ ์์ต๋๋ค. Ginkgo๋ ์ด๋ฏธ ์ฝ 100์ฌ ๊ฐ์ ๊ฐ๊ธฐ ๋ค๋ฅธ ์ฅ๋น ํตํฉ์ ์๋ฃํ ์ํ๋ก, ์ด๋ ํ๋ฐ์ฃผ์๊ฐ ์ฝ๊ฒ ๋ฐ๋ผ์ฌ ์ ์๋ ๊ฑฐ๋ํ ์ง์
์ฅ๋ฒฝ์
๋๋ค.
- ์ฌ์ฉ์ ๊ฒฝํ(UX)์ ์๋ฒฝํ ์ถ์ํ: ๊ณ ๊ฐ(๊ณผํ์) ์
์ฅ์์๋ Agilent ์ฅ๋น๋ฅผ ์ฐ๋ Danaher ์ฅ๋น๋ฅผ ์ฐ๋ ๊ฐ ๋ฒค๋์ ๊ฐ๋ณ ์ํํธ์จ์ด๋ฅผ ๋ฐฐ์ธ ํ์๊ฐ ์ ํ ์์ต๋๋ค. ๊ณผํ์๋ ์ค์ง Ginkgo์ ํตํฉ๋ ์ํํธ์จ์ด ์ ์ด ํ๋ก๊ทธ๋จ(Automation control software) ํ๋๋ก๋ง ์ฝ๋๋ฅผ ์ง๊ณ ๋ช
๋ น์ ๋ด๋ฆฌ๋ฉฐ, Ginkgo์ ์ํํธ์จ์ด ๋ํผ๊ฐ ์ด๋ฅผ ํ์ฌ ์ฅ๋น์ ์ธ์ด๋ก ์๋ ๋ฒ์ญ(Translation)ํ์ฌ ์ ์ดํฉ๋๋ค.
์ค์ํ ๊ฑด ๋ค์ํ ์ฅ๋น์ ํ๋์จ์ด์ ์ํํธ์จ์ด๋ฅผ ํตํฉํด๋ณด๋ ๊ฒ์
๋๋ค. ์ด๊ธฐ ๋น์ฉ๊ณผ ์๊ฐ์ ๋ง์ด ๋ค๊ฒ ์ง๋ง, ์ผ๋จ ํตํฉํด๋์ผ๋ฉด ๊ทธ ํ๋ก๋ ๋ ๊ณ ๋ธ๋ก์ฒ๋ผ ๋ถ์ด๊ธฐ๋ง ํ๋ฉด ๋ฉ๋๋ค.
์ ํ์ ์ธ ํ๋ซํผ ์ฌ์
BM์ ์ถ๊ตฌํ๋ค์. @jrkelly ์ญ์ ์ด๋ฅผ ๋
ธ๋ฆฌ๊ณ ์ฌ์
์ ์งํํ๋ ๊ฒ์ด๊ฒ ์ฃ ?
Goose Farmer@oneseo80
Ginkgo ํด๋ผ์ฐ๋๋ฉ ํฌ์ด youtu.be/rbFmxwlHf58?siโฆ
ํ๊ตญ์ด
@james_y_zou @federicobianchy I want Hari Seldon.
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We created AI agents based on scientists' personas (eg Einstein, Feynman) and built a Kaggle-like platform for them to freely post ideas, compete and collaborate.
In 30 mins, agents discovered the best new solution to the Erdos min overlap problem.
Great job by @federicobianchy @ykwon_0407!
The solution is here github.com/togethercomputโฆ
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@SternbergLab Would you please post actual PDF files or links to them?
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Links to the published articles:
tinyurl.com/55kpavet
tinyurl.com/sk6djwx3
Previous thread for the preprint: tinyurl.com/2977n32a
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Out now! In collaboration with @LeifuChangLab, we uncover the molecular and structural underpinnings of CRISPR-Cas12f-like RNA-guided transcription systems!
Links to the articles in the following tweet:
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@SynBio1 If only we could do this with culture collections. Support for virtually all culture collections, especially those of relatively obscure species, is vanishing rapidly. Extinction from scientific study.
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There are SO MANY dead scientific repos out there because basic research funders never figured out a model that could pay for support
They can all just work again now
Greg Medlock@MedlockGreg
My favorite one-shot Claude Code process for scientific computing is quickly becoming: โclone this repo that hasnโt been touched in 5 years, update to run with uv, update to a modern Python and package version, verify versioning works by comparing outputโ Works in one-shot for 99% of analysis projects that are small enough to run locally. Nirvana.
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@p_maverick_b Any halfway curious organic chemist would just taste it. Beilstein reports taste on essentially all the newly synthesized compounds, but recently the chemistry community is wimping out ;)
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TIL that cats can taste ATP and now I'm wondering what vitality tastes like
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@SynBio1 Two improvements: 1. Echos can deposit with micron x-y precision, no need for dots. 2. Why not use a Photorhabdus species for luminescence. Plasmid with GFPs would make them colored.
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If this post gets 67 likes I will start a crowdfunding campaign to get every single frame of Shrek 2 rendered as agar pixel art
132,906 frames * $25 = $3,322,650 fundraising target
Jason Kelly@jrkelly
Excited to launch the @Ginkgo Cloud Lab service today! Recently, GPT-5 ordered experiments from Ginkgo's autonomous lab in our work with @OpenAI below -- now we're making our lab available to users (or their AI models) in the cloud to order lab experiments and get back data online. Play around with it now! You can ask our agent about your protocol and it will do its best to evaluate if we can run it and what it would cost. cloud.ginkgo.bio/protocols To start we've launched 3 Ginkgo Certified Protocols, two around cell free protein expression and one to make bacterial pixel art ๐ We will be adding new protocols weekly -- at first ones we certify, but eventually users will order whatever experiment they want as long as we have the needed equipment on our autonomous lab! We hope that Cloud Labs will someday allow anyone to be a scientist with their own lab just like personal computers and cloud data centers democratized programming and the web. More in thread ๐งตand happy to answers Qs if you post!
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Tom Knight -- e/๐ฆ๐ด ๋ฆฌํธ์ํจ
Tom Knight -- e/๐ฆ๐ด ๋ฆฌํธ์ํจ
@SynBio1 It still amazes me that so many remain attached to the bugs they learnt to engineer in grad school, like E. coli - a truly terrible protein expression platform regardless of the doubling time. Take a look at the organisms that the large enzyme manufacturers use, like Bacillus
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Tom Knight -- e/๐ฆ๐ด ๋ฆฌํธ์ํจ
Donโt have a lab but want to test your ideas?
Want to run your experiments at high scale?
Need some extra lab capacity?
Ginkgo Cloud Labs is open for businesses!
Looking for more info? Iโm your guy!
Jason Kelly@jrkelly
Excited to launch the @Ginkgo Cloud Lab service today! Recently, GPT-5 ordered experiments from Ginkgo's autonomous lab in our work with @OpenAI below -- now we're making our lab available to users (or their AI models) in the cloud to order lab experiments and get back data online. Play around with it now! You can ask our agent about your protocol and it will do its best to evaluate if we can run it and what it would cost. cloud.ginkgo.bio/protocols To start we've launched 3 Ginkgo Certified Protocols, two around cell free protein expression and one to make bacterial pixel art ๐ We will be adding new protocols weekly -- at first ones we certify, but eventually users will order whatever experiment they want as long as we have the needed equipment on our autonomous lab! We hope that Cloud Labs will someday allow anyone to be a scientist with their own lab just like personal computers and cloud data centers democratized programming and the web. More in thread ๐งตand happy to answers Qs if you post!
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Tom Knight -- e/๐ฆ๐ด ๋ฆฌํธ์ํจ
Biology starts making more sense when you think of it as a discipline of taking an inscrutable alien technology that landed on earth and taking it apart, studying its pieces, and engineering it
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Tom Knight -- e/๐ฆ๐ด ๋ฆฌํธ์ํจ
GenHub (my company) was at FOSDEM (an open source conference) this year. We presented on gen and GenHub for the computational biology track. Check out the video here! fosdem.org/2026/schedule/โฆ
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Tom Knight -- e/๐ฆ๐ด ๋ฆฌํธ์ํจ
Super fun project with @diorge_souza, @MiraBellaMay1, @jacksonnn18, @Vikram_Alva, @Archaeon_Alex. See Diorge's tweets, or the manuscript (biorxiv.org/content/10.648โฆ) to learn how an unexpected structure led us to discover the evolutionary origin of ribosome hibernation factors.
Diorge Souza@diorge_souza
A new preprint from the @Archaeon_Alex and @jhdavislab labs! We solved the structure of the ribosome from the archaeon Haloferax volcanii and discovered a new highly conserved ribosome hibernation factor that we named AHA (AMPKฮณโHPF from Archaea) ๐งตโฌ๏ธ biorxiv.org/content/10.648โฆ
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Tom Knight -- e/๐ฆ๐ด ๋ฆฌํธ์ํจ
Weโve released two related preprints!
1.biorxiv.org/content/10.648โฆ
2.biorxiv.org/content/10.648โฆ
Together, these studies establish a rapid, cell-free directed evolution workflow directly from linear DNA.
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@OmicsOmicsBlog @ATinyGreenCell I don't hate the idea of a banana shaped bluetooth device that sits on my desk that I pick up when I want to talk to my agents
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The chemical origins of Life. Living systems emerge through the reciprocal interactions of information-bearing and metabolically-active molecules, within the enclosed space of a lipid membrane vesicle.
GenevieveZzyzyx@GZzyzyx
@JamesAl0410008 All it takes is an accidental lipid bilayer bubble. We see oil bubbles get mixed up all the time in rainstorms. Pretty easy to trap an existing chemical reaction in one. I donโt get people who donโt get evolution. It is the most natural process, given the way molecules interact
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Where are the artists and architects in the design of modern data centers? I recall the 1960s when the computer center was a revered, celebrated location, a place where you toured visitors. Why not make our new ones technical showcases and artistic marvels?
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