@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/🦀🌴
1.2K posts
Tom Knight -- e/🦀🌴
@TomKnightSynBio
Engineer of stuff that is alive or computes. Follow us all to that blue place.
Bergabung Ocak 2021
3.7K Mengikuti3K Pengikut
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/🦀🌴 me-retweet
First in Human! When @rhomsany and I first started Octant, this was the dream. A platform that makes molecules that few others can go after… 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-an…
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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. Cocioba🪄🌷@ATinyGreenCell
Let's extract some DNA from a petunia leaf together! 🧬🧵 1/n
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Tom Knight -- e/🦀🌴 me-retweet
영상을 보고나니, Ginkgo RAC의 해자는 하드웨어 래퍼(hardware wrapper), 소프트웨어 래퍼(software wrapper)네요.
기존의 바이오 장비 시장은 Thermo Fisher, Agilent, Danaher 등 각 벤더가 자신들만의 폐쇄적인 규격과 소프트웨어를 고집하여 호환성이 떨어지는 파편화된 시장이었습니다.
Ginkgo는 이질적인 타사 장비들을 자신들의 '래퍼(Wrapper)'로 감싸서 완벽하게 통합된 하나의 시스템으로 탈바꿈시켜버립니다.
1. 하드웨어 래퍼 (Hardware Wrapper): 파편화된 장비의 '레고 블록화'
RAC은 일종의 '표준화된 껍질(Standardized wrapper / envelope)’입니다.
- 물리적 인터페이스의 통일: 시중에 판매되는 원심분리기, 배양기, 액체 분배기 등은 크기와 모양이 모두 다릅니다. Ginkgo는 이 개별 장비들을 6축 로봇 팔과 자가부상 샘플 운송 트랙(Magnumotion track)이 장착된 표준화된 카트(RAC) 안에 집어넣고 감싸버립니다.
- 복제 및 확장성의 해자: 특정 장비(예: 플레이트 실러)를 RAC에 맞게 통합하는 초기 설계(프레임 및 앵커 포인트 개발)를 한 번 완료하고 나면, 이후부터는 추가 R&D 없이 그저 “복붙(copy and paste)" 하듯 찍어내어 비용과 시간을 획기적으로 줄일 수 있습니다. 이로 인해서 고객이 원하면 언제든 새로운 기능을 레고블록처럼 쉽게 추가할 수 있습니다.
2. 소프트웨어 래퍼 (Software Wrapper): '끔찍한(Heinous)' 벤더 소프트웨어의 추상화
하드웨어 통합보다 훨씬 더 강력한 해자는 바로 소프트웨어 단에서 발생합니다.
- 폐쇄적인 벤더 API의 극복: 많은 장비 벤더들은 타사의 통합을 막고 자사 소프트웨어만 쓰게 하려고 의도적으로 API를 제공하지 않거나 폐쇄적으로 운용합니다. Ginkgo는 고객이 요청하는 장비를 시스템에 올리기 위해 직접 드라이버를 개발하거나 장비에 하드와이어링(Hardwire)하는 고된 작업을 수행합니다. 장비 하나를 통합하는 데 1~2개월이 걸리는 힘든 과정이지만, 한 번 통합해 놓으면 영구적으로 시스템에서 사용할 수 있습니다. Ginkgo는 이미 약 100여 개의 각기 다른 장비 통합을 완료한 상태로, 이는 후발주자가 쉽게 따라올 수 없는 거대한 진입 장벽입니다.
- 사용자 경험(UX)의 완벽한 추상화: 고객(과학자) 입장에서는 Agilent 장비를 쓰든 Danaher 장비를 쓰든 각 벤더의 개별 소프트웨어를 배울 필요가 전혀 없습니다. 과학자는 오직 Ginkgo의 통합된 소프트웨어 제어 프로그램(Automation control software) 하나로만 코드를 짜고 명령을 내리며, Ginkgo의 소프트웨어 래퍼가 이를 타사 장비의 언어로 자동 번역(Translation)하여 제어합니다.
중요한 건 다양한 장비의 하드웨어와 소프트웨어를 통합해보는 것입니다. 초기 비용과 시간은 많이 들겠지만, 일단 통합해놓으면 그 후로는 레고블록처럼 붙이기만 하면 됩니다.
전형적인 플랫폼 사업 BM을 추구하네요. @jrkelly 역시 이를 노리고 사업을 진행하는 것이겠죠?
Goose Farmer@oneseo80
Ginkgo 클라우드랩 투어 youtu.be/rbFmxwlHf58?si…
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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/togethercomput…
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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: “clone this repo that hasn’t been touched in 5 years, update to run with uv, update to a modern Python and package version, verify versioning works by comparing output” 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 😀 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 🧵and happy to answers Qs if you post!
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Tom Knight -- e/🦀🌴 me-retweet
Tom Knight -- e/🦀🌴 me-retweet
@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/🦀🌴 me-retweet
Don’t 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? I’m 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 😀 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 🧵and happy to answers Qs if you post!
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Tom Knight -- e/🦀🌴 me-retweet
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/🦀🌴 me-retweet
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/…
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Tom Knight -- e/🦀🌴 me-retweet
Super fun project with @diorge_souza, @MiraBellaMay1, @jacksonnn18, @Vikram_Alva, @Archaeon_Alex. See Diorge's tweets, or the manuscript (biorxiv.org/content/10.648…) 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 (AMPKγ–HPF from Archaea) 🧵⬇️ biorxiv.org/content/10.648…
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Tom Knight -- e/🦀🌴 me-retweet
We’ve released two related preprints!
1.biorxiv.org/content/10.648…
2.biorxiv.org/content/10.648…
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 don’t get people who don’t 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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