My name is James, @techninja on Github, and I'm a long time HN watcher and learner. Just this past 6 months I decided crazily to follow some random thought I had about trying to do anything with my DNA data, now I guess it kinda works good enough to show ya? Let's see what you think.
It's an open source, client-side polygenic scoring tool and imputation pipeline for common traits (64 right now), see data pipeline at https://github.com/techninja/asili-lab.
When I thought of this thing as somethign that people could use, I clearly saw that no one is willing to go find their file just to hand it to some server where it could be linked to your online tracking IDs and their own trait research. This kinda flips that on its head, I did all the work to compile the PGS variant collections for each trait as listed on the PGS catalog, a single file per trait split by chromosome is scored directly (with fast liftover from hg19->hg38 positions), letting you score your local DNA against gigabytes of weighted variants for all of the identified traits through cheap cloudflare R2 CDN byte range sipping (and hosted on cloudflare pages free tier!).
The benefits of the architecture are pretty obvious as far as simplified hosting and prep for me, but the benefits for the user are huge without needing to risk data breech or willful corporate data selling. Their data stays put locally for them, their mobile phone or laptop is the compute through DuckDB-wasm and Using a 10 year old machine and a single core I can score 64 traits for a user in ~3 hours.
The data pipeline lab work also has my best bet at a near identical output and process as Michigan Imputation Server (https://imputationserver.sph.umich.edu/), running locally from downloaded publically available genome data (~300-500gb?). I'm offering to run the pipeline pre-configured in AWS for a little cost (https://impute.asili.dev/about), my first personal AWS and Stripe integration project! Scare-cited for sure.
Even worse, I couldn't stand to put yet another React project out into the world, so I collected all the crap I'd learned doing web dev since the 90s to make some kind of modern, no build, collection of ideas I call Clearstack (https://clearstacks.org/). Asili, and of these sites I maintain (and my personal blog) are running this scaffolding spec framework to great success, but it might still be a stupid idea, so don't go jumping on the wagon yet.
I am a solo maintainer, and I'm sharing this as a beta to gather feedback from bioinformaticians, developers, and self-hosters. The repository is here: https://github.com/techninja/asili
I would love feedback on:
* Any bottlenecks or issues for certain machines.
* Thoughts on no-build dev architecture
* Any related projects I can look into
I'll be around to answer questions, handle technical feedback, and review suggestions!
What a beautiful hack by nature. I wonder if you could create a lens with a similarly shaped pupil/iris and see the chromatic aberration in a black and white camera correctly focused on the output. Would make for a fun weekend project :)
Abstracted color getters! This seems to be the biggest issue with users. You have to wet the brush and wiggle on the color to actually get anything on the brush. They can't seem to get that far.
I'd love to implement your work in RoboPaint, might even be able to pull some color information to make portraits from black sharpie outline with your implementation and watercolor fill. I've completely failed at any attempts to make decent raster -> paint vector so far.
And joshu was too! Talked to him about drawing algos. He's too smart for his own good ;)
Oh I would probably do something along the lines of adding simple shapes (Circle x/y & radius, ETC), auto re-inking of last color for long lines... and who knows what else. I ran out of time to work on it.
HA! Well, that's hilarious. I was just talking to @eliot at Hackaday supercon about making this with WaterColorBot and CNCserver at his suggestion, I guess if it's out there it's out there. Definitely a different setup than I would have done, but it seems like it might work.
Really though this is just asking for people to write interfaces and use twitch IRC chat as a terrible API. I'm forced to think that only when it's unpopular (but popular enough), anything resembling what a user intends will be created. At least in the end you're guaranteed to get art.
Oh dear... Might have to build this now hmm? I'm not sure it counts if it's got a arduino in it and a cat 5 sticking out the back. The water is also an issue.
I check the oursignal.com aggregator regularly (though the delicious.com content it adds is of seriously dubious quality). The hackernews and reddit posts are almost always interesting, insightful, or relating to what I do (full time+ contract web dev).
Glad to hear there's more hacker dads out there, it's hard to find them sometimes! I'm glad we have such a diverse audience, and if we can get more of the right kind of audience in (those that not only watch, but -actually- get out there and make something with their kids) then the point will be just. We want to hear "Hey look what I did with my kids!".
Some of the projects tend to aim for the lazy or skeptical, trying to make it -so- easy you've got -no- reason not to go spend time making (and possibly failing) with your kids. Adam Savage's "Failure is always an option" motto stands with us everywhere we go. If you're not failing, you're probably not learning.
Yep. Making a show is in itself an amazing discovery of what you could do. We keep everything simple, the script is only a basic guideline and she takes an active role in every part of the production.
I'm simply hopeful that as she blossoms into adulthood, some of the adventures her and I share in her youth help her out in the rest of her life.
Great to see the hacker news crowd has found the show entertaining and useful! We glossed over a lot of the programming aspect because the physical aspect of making something is far more immediately comprehensible for kids (which is why we emphasize getting out and making -something- above all else).
We made sure to get the source code as commented and as easy to handle as possible, but introducing it in the video not only requires a substantial programming background overhead, but may scare a number of newbies off a lot quicker than if they just copied and pasted something into an simple IDE.
Getting something working, that kids can feel some kind of accomplishment with, no matter how simple, can psychologically push them over the initial barrier of fear that an come with new, seemingly difficult things.
The Arduino itself as a dev board platform does a great job of erasing a lot of that fear with a friendly usb connection, holes you can plug things directly into and an open IDE with only a few simple buttons and configurations. The remaining hurdles exist beyond, in attainable projects that lets you poke and prod at the internals and get a good feel for how and why something works, or how to break it. Hopefully our little starter project are simple enough to get kids (or anyone for that matter) out there and -trying something-, no matter how silly or simple. If all you do is do something once and never again, you are still the better for doing it.
My name is James, @techninja on Github, and I'm a long time HN watcher and learner. Just this past 6 months I decided crazily to follow some random thought I had about trying to do anything with my DNA data, now I guess it kinda works good enough to show ya? Let's see what you think. It's an open source, client-side polygenic scoring tool and imputation pipeline for common traits (64 right now), see data pipeline at https://github.com/techninja/asili-lab.
When I thought of this thing as somethign that people could use, I clearly saw that no one is willing to go find their file just to hand it to some server where it could be linked to your online tracking IDs and their own trait research. This kinda flips that on its head, I did all the work to compile the PGS variant collections for each trait as listed on the PGS catalog, a single file per trait split by chromosome is scored directly (with fast liftover from hg19->hg38 positions), letting you score your local DNA against gigabytes of weighted variants for all of the identified traits through cheap cloudflare R2 CDN byte range sipping (and hosted on cloudflare pages free tier!).
The benefits of the architecture are pretty obvious as far as simplified hosting and prep for me, but the benefits for the user are huge without needing to risk data breech or willful corporate data selling. Their data stays put locally for them, their mobile phone or laptop is the compute through DuckDB-wasm and Using a 10 year old machine and a single core I can score 64 traits for a user in ~3 hours.
The data pipeline lab work also has my best bet at a near identical output and process as Michigan Imputation Server (https://imputationserver.sph.umich.edu/), running locally from downloaded publically available genome data (~300-500gb?). I'm offering to run the pipeline pre-configured in AWS for a little cost (https://impute.asili.dev/about), my first personal AWS and Stripe integration project! Scare-cited for sure.
Even worse, I couldn't stand to put yet another React project out into the world, so I collected all the crap I'd learned doing web dev since the 90s to make some kind of modern, no build, collection of ideas I call Clearstack (https://clearstacks.org/). Asili, and of these sites I maintain (and my personal blog) are running this scaffolding spec framework to great success, but it might still be a stupid idea, so don't go jumping on the wagon yet.
I am a solo maintainer, and I'm sharing this as a beta to gather feedback from bioinformaticians, developers, and self-hosters. The repository is here: https://github.com/techninja/asili
I would love feedback on: * Any bottlenecks or issues for certain machines. * Thoughts on no-build dev architecture * Any related projects I can look into
I'll be around to answer questions, handle technical feedback, and review suggestions!