Timothy Stiles (@TimothyStiles) header
Timothy Stiles (@TimothyStiles) profile picture

Timothy Stiles

@TimothyStiles

Building the world's most modern, open source, software library for genetic engineering. https://xitter.cf/t.co/2QktmNwjOg…

 San Francisco, CA
stiles.io
Joined January 2012
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  • Followers3K
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Photo by Timothy Stiles (@TimothyStiles)Photo by Timothy Stiles (@TimothyStiles)Photo by Timothy Stiles (@TimothyStiles)Photo by Timothy Stiles (@TimothyStiles)Photo by Timothy Stiles (@TimothyStiles)Photo by Timothy Stiles (@TimothyStiles)Photo by Timothy Stiles (@TimothyStiles)Photo by Timothy Stiles (@TimothyStiles)Photo by Timothy Stiles (@TimothyStiles)
Timothy Stiles retweeted
Wei Shen (@shenwei356) profile picture
Wei Shen@shenwei35625 Oct 2024
Looks useful. Poly project from @TimothyStiles has a Golang pkg 'seqhash' (github.com/bebop/poly/tree/m…) as well, and seqkit has a 'sum' cmd for the whole fasta/q file, both supporting circular/linear, single/double-stranded seqs (bioinf.shenwei.me/seqkit/usa…). biorxiv.org/content/10.1101/…
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To all my friends in town for synbiobeta: Love y'all and want to see your faces but I'm sick and don't want to give y'all conference cough 😷
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I want to hire this kid.
Michael Levin (@drmichaellevin) profile pictureMichael Levin
@drmichaellevin25 May 2021
I once gave a talk to a class of 9-10 year olds on morphogenetic plasticity. One raised his hand & asked: could we make a flying rhinoceros? I gave him the reasons why it was unlikely. Rightly shaming me for a lack of commitment, he said "so what, you're just giving up??!"
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Meme driven development
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Depends on how fast I can do the live demo but the talk I gave at synbiobeta the other year averaged out to a rate of 1 unique SpongeBob meme appearing every 18.75 seconds.
SpongeBob diaper meme template. First panel - Patrick Star: "Synbio software isn't that bad" Second panel - Spongebob holding a trashcan full of dirty diapers label Genbank. 3rd - SB points to pile of dirty diapers labeled "Code available upon request". 4th: SB open fridge full of diapers labeled, "abandonware. 5th: SB reveals that couch is made of diapers labeled, "no unit testing or documentation. 6th: SB peels back wall paper revealing that his house's wall are stuffed with dirty diapers labeled, "it runs on my machine". 7th: SB points out the window to something the viewer can't see in frame 8th: Camera pulls back to reveal a giant pile of diapers on SpongeBobs lawn labeled, "Mountain of Spaghetti Code".

ALT SpongeBob diaper meme template. First panel - Patrick Star: "Synbio software isn't that bad" Second panel - Spongebob holding a trashcan full of dirty diapers label Genbank. 3rd - SB points to pile of dirty diapers labeled "Code available upon request". 4th: SB open fridge full of diapers labeled, "abandonware. 5th: SB reveals that couch is made of diapers labeled, "no unit testing or documentation. 6th: SB peels back wall paper revealing that his house's wall are stuffed with dirty diapers labeled, "it runs on my machine". 7th: SB points out the window to something the viewer can't see in frame 8th: Camera pulls back to reveal a giant pile of diapers on SpongeBobs lawn labeled, "Mountain of Spaghetti Code".

Arye Lipman (@aryelipman) profile pictureArye Lipman
@aryelipman15 Apr 2024
Replying to @TimothyStiles @PracheeAC @AsteraInstitute @koeng101
how many spongebob memes will be featured in said talk
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I remember the first meetup I ever went to in the Bay Area had steak, mezcal, a DJ, and a dude who figured out how to run windows 98 in the browser via web assembly showing off for 150 nerds. We used to be a community, a proper community.
Timothy Stiles (@TimothyStiles) profile pictureTimothy Stiles@TimothyStiles29 Mar 2024
Thinking about making a local meetup in SF called, "Anything but Beer, Pizza, and AI", because it's getting dismal out here folks.
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Thinking about making a local meetup in SF called, "Anything but Beer, Pizza, and AI", because it's getting dismal out here folks.
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tired: longevity research wired:
Image from Timothy Stiles (@TimothyStiles)
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Feels like there should be a regression test for this.
Kieran Samuk (@ksamuk) profile pictureKieran Samuk@ksamuk6 Feb 2024
PSA, since I've now seen problems arising from this: As of Sept 2023, GATK no longer makes missing genotypes explicit in VCFs (i.e. "./." as in the VCF spec). Missing genotypes are instead coded as "0/0" with a DP=0 format field. See attached for examples.
Image from Kieran Samuk (@ksamuk)
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Do it with @ollama I've got llama2 running on a 16gb macbook air right now and the most difficult part of setup was waiting for the model to download.
Tyler Maran (@TylerMaran) profile pictureTyler Maran
@TylerMaran29 Jan 2024
are LLMs going to drive a swing back to on prem? i'm looking at $970/mo on AWS for the equivalent compute of my 16gb macbook seriously thinking of just buying two more macbooks and running omni from my living room
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There was a certain 𝒋𝒆 𝒏𝒆 𝒔𝒂𝒊𝒔 𝒒𝒖𝒐𝒊 to this event hosted by @ollama and @replicate tonight that made it feel really special. Never have I been so excited to go home after an event and build something with CGo.
ollama (@ollama) profile pictureollama
@ollama24 Jan 2024
Super excited for tonight’s Local & open-source AI developer meetup!!
Image from ollama (@ollama)
Image from ollama (@ollama)
Image from ollama (@ollama)
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annnd @ollama built with absolutely 0 errors on the first try with CGo which if you've used CGo before you know is impressive.
A screenshot of completed terminal output when building ollama from scratch with CGo.

ALT A screenshot of completed terminal output when building ollama from scratch with CGo.

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in awe of the size of this lad. what to do with this electric motor? lime for scale.
a 9 1/2 inch diameter electric motor kind of like the the ones you see on quadrotors but huge.

ALT a 9 1/2 inch diameter electric motor kind of like the the ones you see on quadrotors but huge.

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everytime I see a code coverage badge above 90% on a git repo I get an unreasonable feeling of joy
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when one of your repos is getting more stars and traffic than usual but you have no idea why
two panels First panel: awkward monkey puppet looking to the side from a profile view. Second panel: awkward monkey puppet looking forward from a profile view https://knowyourmeme.com/memes/awkward-look-monkey-puppet

ALT two panels First panel: awkward monkey puppet looking to the side from a profile view. Second panel: awkward monkey puppet looking forward from a profile view https://knowyourmeme.com/memes/awkward-look-monkey-puppet

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temporarily forgot that I write things in Go to avoid containers in general and had a 𝒗𝒆𝒓𝒚 𝒃𝒂𝒅 𝒕𝒊𝒎𝒆™
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So @TwFlem made a PR for this absolutely bad*ss burrows-wheeler transform implementation based on @BenLangmead's youtube videos. github.com/bebop/poly/pull/4… I don't know enough about bwt to give this PR the review it deserves. Anyone here on this bird app who could lend us a hand?
#360 Bwt by TwFlem · Pull Request #411 · bebop/poly

#360 Bwt by TwFlem · Pull Request #411 · bebop/poly

Changes in this PR This is for #360. @TimothyStiles mentioned implementing a naive version of the BWT. At first I took his suggestion. As I read up on the applications of BWT for genomic data, the ...

github.com
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Will also stress that @TwFlem wrote this for correctness. Don't worry if it isn't speed optimized yet there's stuff in the works for that.
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Tyler Maran (@TylerMaran) profile pictureTyler Maran
@TylerMaran21 Dec 2023
twitter when @TimothyStiles is back youtube.com/shorts/P45tZCfx_…
honkin 🎷 #animation #pokemon #cg #epic #sax #squirtle #guy

honkin 🎷 #animation #pokemon #cg #epic #sax #squirtle #guy

Enjoy the videos and music you love, upload original content, and share it all with friends, family, and the world on YouTube.

youtube.com
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there's absolutely no way that intelligence agencies haven't at least tried to contract the geoguesser guy
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guy is a living reminder to not post photos with my windows open unless I want the whole world to know where I live
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