Seth Howes @SethSHowes
🩺 doctor defected to tech 👨🏼💻 prev engineer @exolabs | medicine @uniofoxford | ML @imperialcollege github.com/sethhowes Joined August 2021-
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perhaps Anthropic are overreacting by blocking fable usage for bio oh wait…
I just sequenced a human genome to 30× coverage entirely at home. As far as I know, this is the first time this has been done. I didn’t step foot in a lab once. Every step - from saliva collection, to running the sequencer - took place in a single room with a dining table +
Today, we are launching our research blog! We’ll use it for technical notes from our work building tools for enzyme and biomolecular design. Our first post is about The Unreasonable Redundancy of Nature's Protein Folds. TLDR: Please don't fold more sequences (1/n)
yes.
My latest article is about how the longevity movement should not be about wellness tips and tricks and lifestyle improvements, but rather, true, biotech-enabled life extension and life improvement. We should be able to live exciting lives, without restriction. Forever.
This is a great point. I spent $180 on compute alone for base + variant calling. If I were saving the data in the cloud I would also be paying $70 per sequence per month. You could probably charge a 30% margin on this. My guess is that they haven’t done this as they believe it’s hard to build this product well. According to people I’ve spoken to at nanopore, they have to service a lot of technical issues from people that have P2 Solos. Usually root issue is lack of onboard compute, with poor product UX to ameliorate potential failure modes. Plenty that can go wrong when a flow cell produces 900 gb of data per flow cell & you have such variability in internet upload speeds / reliability. This isn’t to say it’s not possible - I think it definitely is. You could have a robust system for uploads that is tolerant to interruptions. If you consistently face internet reliability issues as a user then you could be prompted in MinKNOW to buy a compute module instead.
Checked out of my hotel room but no worries - I can keep sequencing. I’m eking out that final 5% data yield in the hotel lobby before my flight in 3 hours. This is truly sequencing anywhere. Maybe i should keep sequencing at 30,000 feet…
@billytcl Not if you upload to R2 as the object store - they don’t charge egress fees whereas S3 does
@billytcl stream pod5 files to GPU box on runpod!
@The__Taybor now a sequencer sequencing in space is seriously cool
@kirk3gaard @The__Taybor @ollama @exolabs @__tinygrad__ this too
@The__Taybor @kirk3gaard @ollama This is what @exolabs are working on (where I used to work)
@kirk3gaard @brad_woolf @TheODINInc I built a relay agent + remote gpu worker that makes it super easy to offload basecalling. If this is useful for community then happy to share
@KianSadeghi5 @mattzieger @Gencove @nucleusgenomics reasonable
I just sequenced a human genome to 30× coverage entirely at home. As far as I know, this is the first time this has been done. I didn’t step foot in a lab once. Every step - from saliva collection, to running the sequencer - took place in a single room with a dining table + kitchenette. Six weeks ago, I had never done wet lab biology before. I used an Oxford Nanopore P2 Solo - the only commercially available sequencing device portable enough to do 30x human genome sequencing at home. Biggest takeaway - I could build something that combined software, hardware, and molecular biology far faster than I thought was possible. I can name >100 specific instances where AI helped me solve a technical problem that would previously have blocked me because I lacked access to a domain expert. For example: how do I save my sequencing run when my DNA extraction yield is 4x lower than I need it to be, and I have this limited set of reagents to hand? To make this work, I had to navigate multiple disciplines: - writing software to monitor sequencing runs and orchestrate remote GPU infra for basecalling - learning + executing 5 hour long molecular biology protocols - building a hardware device to quantify DNA concentration Apologies for the hyperbole, but I feel super lucky to be living in 2026. A few weeks ago I decided to sequence a human genome to 30x at home. Then I actually did it. And I did it really quickly.
@Scobleizer now at 5 full sequences in 3 days - all in single hotel room
@KianSadeghi5 @mattzieger @Gencove @nucleusgenomics How much do you charge for 30x WGS?
@lvwerra i would like to, but i have yet to find a way for them to be useful for personal genome variant interpretation. i would love to hear any ideas you have on how they might be
@antinertia may livestream a sequencing run start to finish later this week if people want
@antinertia claude & brain is all you need
@WillThings @YimbyGeorge SAVE THE P2 SOLO
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