Bradley Woolf

677 posts

Bradley Woolf banner
Bradley Woolf

Bradley Woolf

@brad_woolf

programming biology

California, USA 가입일 Nisan 2017
402 팔로잉183 팔로워
Andrew Beggs
Andrew Beggs@adbeggs·
💥💥💥BOOM . Well then. I’m not sure what @nanopore have been putting in their flowcells but Luke Ames and @JoStockton1 have set a new internal record for the highest flowcell output we’ve even seen from a R10.4.1 flowcell on a fresh frozen SOLID tumour 👉 200.86gbases from a single run 👉 No flush and reload 👉 New England Biolabs enzymatic Ultrashear 👉 N50 of 6.5kbases 👉 Run for just over 3 days Most of the flowcells on our P24 performed like this, with > 180gbases, so much so that one of our empty P24 very nearly ran out of space running at full capacity. In the end we generated 68tb of data (including POD5).. quite the output! Well done Luke and Jo
Andrew Beggs tweet mediaAndrew Beggs tweet media
English
3
6
18
1.7K
Clive G. Brown
Clive G. Brown@The__Taybor·
When i dreamt up this device, it was meant as a ‘cross-over’ design between lab and field use. Yes a skilled at home user can just about do it. But the limiting thing is the sample/library preparation that still relies on standard, albeit basic, lab ware. I did intend to design out and/or automate that stuff making non-lab use much easier. Never got to finish it although I’m currently working on something similar. Sample/library preps tend to be ‘green-fingered’, thats where a lot of the variability in yield comes from, like baking cakes, they’re never quite the same. That’s molecular biology for you. Needs simplifying. I think i was the first person to sequence their own genome end-to-end on this technology several years ago. My public domain genome has been used to teach students genetics.
English
2
1
14
703
Seth Howes
Seth Howes@SethSHowes·
I’ve wanted to do this for a decade. But I never did - I refuse to give any company my DNA. It is me. So this week I sequenced my genome entirely at home. Literally on my kitchen table. I never exposed my DNA sequence to the internet. Not at any point. I used a MinION to do the sequencing (it’s smaller + weighs less than an iPhone). I used open-source DNA models for the analysis (Evo2 and AlphaGenome) running locally on a DGX Spark and Mac Studio. I traced mechanisms behind my family’s multigenerational autoimmune conditions that no clinician has been able to understand. When I set out to do this I didn’t know if it would actually work. It does. Your genome is the most private data you will ever have. You probably shouldn’t let it leave your house.
Seth Howes tweet mediaSeth Howes tweet mediaSeth Howes tweet media
Patrick Collison@patrickc

I'm lucky enough to have a great doctor and access to excellent Bay Area medical care. I've taken lots of standard screening tests over the years and have tried lots of "health tech" devices and tools. With all this said, by far the most useful preventative medical advice that I've ever received has come from unleashing coding agents on my genome, having them investigate my specific mutations, and having them recommend specific follow-on tests and treatments. Population averages are population averages, but we ourselves are not averages. For example, it turns out that I probably have a 30x(!) higher-than-average predisposition to melanoma. Fortunately, there are both specific supplements that help counteract the particular mutations I have, and of course I can significantly dial up my screening frequency. So, this is very useful to know. I don't know exactly how much the analysis cost, but probably less than $100. Sequencing my genome cost a few hundred dollars. (One often sees papers and articles claiming that models aren't very good at medical reasoning. These analyses are usually based on employing several-year-old models, which is a kind of ludicrous malpractice. It is true that you still have to carefully monitor the agents' reasoning, and they do on occasion jump to conclusions or skip steps, requiring some nudging and re-steering. But, overall, they are almost literally infinitely better for this kind of work than what one can otherwise obtain today.) There are still lots of questions about how this will diffuse and get adopted, but it seems very clear that medical practice is about to improve enormously. Exciting times!

English
392
980
12.3K
2.2M
Patrick Collison
Patrick Collison@patrickc·
I'm lucky enough to have a great doctor and access to excellent Bay Area medical care. I've taken lots of standard screening tests over the years and have tried lots of "health tech" devices and tools. With all this said, by far the most useful preventative medical advice that I've ever received has come from unleashing coding agents on my genome, having them investigate my specific mutations, and having them recommend specific follow-on tests and treatments. Population averages are population averages, but we ourselves are not averages. For example, it turns out that I probably have a 30x(!) higher-than-average predisposition to melanoma. Fortunately, there are both specific supplements that help counteract the particular mutations I have, and of course I can significantly dial up my screening frequency. So, this is very useful to know. I don't know exactly how much the analysis cost, but probably less than $100. Sequencing my genome cost a few hundred dollars. (One often sees papers and articles claiming that models aren't very good at medical reasoning. These analyses are usually based on employing several-year-old models, which is a kind of ludicrous malpractice. It is true that you still have to carefully monitor the agents' reasoning, and they do on occasion jump to conclusions or skip steps, requiring some nudging and re-steering. But, overall, they are almost literally infinitely better for this kind of work than what one can otherwise obtain today.) There are still lots of questions about how this will diffuse and get adopted, but it seems very clear that medical practice is about to improve enormously. Exciting times!
English
483
629
9.5K
3.8M
Liam Zebedee
Liam Zebedee@liamzebedee·
One crazy realisation to me is that in 10yrs, everyone will have their DNA fully sequenced. Cost right now is like $7k to DIY it ($3k Oxford Nanopore + ~8 flow cells to get full coverage + some bits and bobs) BGI in China is bringing this down to $100 per test this year
Patrick Collison@patrickc

By the way, I don't know of any great, easy-to-recommend D2C consumer genome sequencing service. Are there any good ones? (We tried @DanteLabs, but never actually got the sequenced genome back, and never heard back from customer support. I encountered someone else who also had this experience with them. @smart_genome ended up working well, but I think they require going through a clinician.)

English
6
4
87
49.5K
Bradley Woolf
Bradley Woolf@brad_woolf·
@btnaughton Wait so did you only do mB or did you stitch all of them together to represent your whole genome?
English
1
0
1
114
Dwarf
Dwarf@Throrf·
@liamzebedee Much cheaper on Plasmidsaurus (no affiliation, I just like the service)
English
1
0
0
365
andrew
andrew@armillspaugh·
@KianSadeghi5 @TuckerCarlson i havent worked in the field in about 15 years but, at least at that point, the part that made these sort of analyses difficult was that we just didn't know what most of the genome did. has the knowledge of the genome changed by an order of magnitude in that time?
English
1
0
0
223
Kian Sadeghi
Kian Sadeghi@KianSadeghi5·
On @TuckerCarlson we talked a lot about this, why genetics — despite it being the greatest preventative medicine tool ever — has been so under appreciated for so long. Our customers more and more are using the data they get from Nucleus alongside AI for amazing health insights (all raw data is available to all customers in a simple download format, they usually port that over into Claude seamlessly).
Patrick Collison@patrickc

I'm lucky enough to have a great doctor and access to excellent Bay Area medical care. I've taken lots of standard screening tests over the years and have tried lots of "health tech" devices and tools. With all this said, by far the most useful preventative medical advice that I've ever received has come from unleashing coding agents on my genome, having them investigate my specific mutations, and having them recommend specific follow-on tests and treatments. Population averages are population averages, but we ourselves are not averages. For example, it turns out that I probably have a 30x(!) higher-than-average predisposition to melanoma. Fortunately, there are both specific supplements that help counteract the particular mutations I have, and of course I can significantly dial up my screening frequency. So, this is very useful to know. I don't know exactly how much the analysis cost, but probably less than $100. Sequencing my genome cost a few hundred dollars. (One often sees papers and articles claiming that models aren't very good at medical reasoning. These analyses are usually based on employing several-year-old models, which is a kind of ludicrous malpractice. It is true that you still have to carefully monitor the agents' reasoning, and they do on occasion jump to conclusions or skip steps, requiring some nudging and re-steering. But, overall, they are almost literally infinitely better for this kind of work than what one can otherwise obtain today.) There are still lots of questions about how this will diffuse and get adopted, but it seems very clear that medical practice is about to improve enormously. Exciting times!

English
5
1
31
27.4K
Thomas Allen
Thomas Allen@ElderAtropos99·
@patrickc @DanteLabs I used Dante a while back and waited almost 6 months for my WGS, but they eventually sent me a hard disk with a 400 GB file and it was worth it. I use a bunch of tools to analyse my VCF incl Promethease, VarSome, etc.
English
1
0
3
364
Patrick Collison
Patrick Collison@patrickc·
By the way, I don't know of any great, easy-to-recommend D2C consumer genome sequencing service. Are there any good ones? (We tried @DanteLabs, but never actually got the sequenced genome back, and never heard back from customer support. I encountered someone else who also had this experience with them. @smart_genome ended up working well, but I think they require going through a clinician.)
Patrick Collison@patrickc

I'm lucky enough to have a great doctor and access to excellent Bay Area medical care. I've taken lots of standard screening tests over the years and have tried lots of "health tech" devices and tools. With all this said, by far the most useful preventative medical advice that I've ever received has come from unleashing coding agents on my genome, having them investigate my specific mutations, and having them recommend specific follow-on tests and treatments. Population averages are population averages, but we ourselves are not averages. For example, it turns out that I probably have a 30x(!) higher-than-average predisposition to melanoma. Fortunately, there are both specific supplements that help counteract the particular mutations I have, and of course I can significantly dial up my screening frequency. So, this is very useful to know. I don't know exactly how much the analysis cost, but probably less than $100. Sequencing my genome cost a few hundred dollars. (One often sees papers and articles claiming that models aren't very good at medical reasoning. These analyses are usually based on employing several-year-old models, which is a kind of ludicrous malpractice. It is true that you still have to carefully monitor the agents' reasoning, and they do on occasion jump to conclusions or skip steps, requiring some nudging and re-steering. But, overall, they are almost literally infinitely better for this kind of work than what one can otherwise obtain today.) There are still lots of questions about how this will diffuse and get adopted, but it seems very clear that medical practice is about to improve enormously. Exciting times!

English
91
14
643
179.1K
alex rubinsteyn
alex rubinsteyn@iskander·
@nanopore We did this in Hammer Lab circa 2014 a lot: didn’t get understand enough of the bio but were sure that the software was the important part
English
1
0
7
654
alex rubinsteyn
alex rubinsteyn@iskander·
I love the tech enthusiasm for bio, I think it will be net positive for progress. But…there’s this remarkable blindness Actual biology often recedes from view, miraculous machines for profiling the biology disappear too. All that’s left is the tech-familiar: GPUs and LLMs
Alex Cheema@alexocheema

people are now sequencing their DNA at home, locally on DGX Sparks and Mac Studios. this madlad is running Evo 2, a 40B‑parameter DNA LLM that predicts genome sequences instead of text. local AI is going to unlock a world of creativity. @karpathy’s personal computing v2 is here.

English
6
12
91
16.1K
Kevin McKernan
Kevin McKernan@Kevin_McKernan·
@SethSHowes @christianteagu3 How big is the panel? Whole exome? Probably needed gobs or DNA to sample through Check your methylation status. It’s uniquely doable with ONT
English
2
0
0
437
christian
christian@christianteagu3·
@Kevin_McKernan @SethSHowes Yeah, methylation status is a huge boon with good quality nanopore reads. Darado SUP + methylation analysis would be interesting. Means of deriving useful info, of course, are more contrived for methylation.
English
2
0
1
377
Bradley Woolf
Bradley Woolf@brad_woolf·
@nanome_inc Would you guys eventually be able to do everything a product like Molsoft does?
English
0
0
0
34
Nanome
Nanome@nanome_inc·
NEW with v2.5 : Trajectory Playback ▶️ MD trajectories live in 4D. Three spatial axes, one temporal. A flat screen shows you a slice of a slice. Step into XR and view conformational sampling, cryptic pockets, and backbone breathing like never before
English
4
11
59
4.5K
Anshul Kundaje
Anshul Kundaje@anshulkundaje·
@brad_woolf The agents are running tools with all kinds of blind spots & variable unquantified reliability + leveraging literature which also has huge reliability issues. I hope you realize this. You would need tons of benchmarking, guardrails in reporting & clinical validation.
English
2
0
3
450
Anshul Kundaje
Anshul Kundaje@anshulkundaje·
This is very bad idea if u don't have the domain expertise to evaluate the reliability of the results yourself or have the patience to dive deep into the results and become a domain expert or have the ability to consult with qualified physicians & genetic counselors.
Patrick Collison@patrickc

I'm lucky enough to have a great doctor and access to excellent Bay Area medical care. I've taken lots of standard screening tests over the years and have tried lots of "health tech" devices and tools. With all this said, by far the most useful preventative medical advice that I've ever received has come from unleashing coding agents on my genome, having them investigate my specific mutations, and having them recommend specific follow-on tests and treatments. Population averages are population averages, but we ourselves are not averages. For example, it turns out that I probably have a 30x(!) higher-than-average predisposition to melanoma. Fortunately, there are both specific supplements that help counteract the particular mutations I have, and of course I can significantly dial up my screening frequency. So, this is very useful to know. I don't know exactly how much the analysis cost, but probably less than $100. Sequencing my genome cost a few hundred dollars. (One often sees papers and articles claiming that models aren't very good at medical reasoning. These analyses are usually based on employing several-year-old models, which is a kind of ludicrous malpractice. It is true that you still have to carefully monitor the agents' reasoning, and they do on occasion jump to conclusions or skip steps, requiring some nudging and re-steering. But, overall, they are almost literally infinitely better for this kind of work than what one can otherwise obtain today.) There are still lots of questions about how this will diffuse and get adopted, but it seems very clear that medical practice is about to improve enormously. Exciting times!

English
13
9
105
29.6K