packeted

Thanks, I appreciate you saying so!

I went with Cloudflare, primarily because I was already using it for a few other projects but I've been incredibly impressed with how it's scaled. I use D1 for my database, Workers for the API and schedule tasks (including using Claude API to pre-review images and submissions), R2 for self hosted OpenStreetmap tiles, encrypted user pet records and images. I use Clerk for auth. Wild that it costs $5/month to serve thousands of users a day.

Both apps are native. I use Leaflet for the web maps and Hugo as the website framework. I'll admit that my CI/CD pipeline is a bit Claude/Codex based which feels a bit fragile at times, but hasn't broken yet.

It's come a long way, the website started as a Leaflet + JSON flatfile with all the map points.

I'm a big fan of Cloudflare and love how they've been improving their interfaces recently. I run a few sites that get 30k uniques a day and it amazes me that I can run them entirely for free - although I now choose to pay $5/month. Their services play very nicely with agents using wrangler and their domains service is top notch. At one point I was a bit netlify proponent but they banned one of my sites without even telling me for an unsubstantiated trademark complaint. Also love that they run 1.1.1.1.

Great initiative. I recently got stung by an advert on reddit for "HBO Max for MacOS, 6 months free" from the official HBO user (don't get me started on how that slipped through). Front and center was a curl | bash copy to clipboard that obfuscated the payload source in base10. I knew better, but I think we've made this kind of thing way too acceptable. Of course it was malware and I realized the instant I pressed enter. Thankfully I didn't give it my password and immediately disconnected from the internet and killed the machine. I'm genuinely concerned these kind of attacks are going to become much more commonplace with AI, plus the ability to inject malicious code in to things that get run by trusted scripted installers.

Files are huge for sure (mine are like 25Gb x 3 of us) but Claude Science / Macbook Pro M5 Max knocked out my analyses in minutes using command line tools like bcftools and scripting. Honestly think this opens up WGS data to much easier analysis and refreshing those analyses in minutes as new discoveries are made.

Thanks for the kind words. Actually we got the trio whole genome sequencing through our neurologist/geneticist a couple of years ago. It was performed by a company called GeneDx. They interpreted the data at the time which is how we got to a diagnosis but knowing I'd want to dive in to it later I asked for the raw data. They provided it as the raw CRAM files and also the VCF (variant call files) which are a bit smaller. But each company has its own pipeline and for example uses different versions of the reference human genome which made working with the data quite hard for me and the people I enlisted. Claude Science seemed to make very easy work of it. Also to be clear, the question I was trying to answer was whether his mutation was likely passed down through my sperm or mom's egg - neither of us have the mutation in our own genomes. Turns out spontaneous (de novo) mutations are much more common in sperm because Spermatogonial stem cells have undergone many more cell divisions over their lives. Everyone has de novo mutations (70+), one of his just happens to be in an unlucky location.

GeneDx aren't direct to consumer so you'd need to get it ordered through a physician but there are some DTC options for example, Dante Labs, Nebula Genomics, Sequencing.com but I can't speak to the quality of their testing.

23andMe doesn't do whole genome or whole exome sequencing. They use a microarray technology that tests for about 650,000 single nucleotide polymorphisms. You can actually download the your raw data on 23andMe and do your own analysis or use a tool like promethease.

I'm an MD so I'm quite comfortable exploring this data and whatever it uncovers. Tools like Claude Science are going to put a lot of power in the hands of every day people, potentially outside the guidance of genetic counseling/docs, which many organizations in the past (including the FDA) have been hesitant to allow.

Marginally but the data manipulation is actually being done locally as the genome CRAM files are like 24Gb each.

I watched the announcement and gave it a spin as I'm a heavy user of cowork/code. So far I'm super impressed. I used it to analyze my whole genome sequencing data I have as my son has a rare genetic condition. I used it to answer a question I'd asked a few bioinformaticians to help me with but never got a satisfactory answer, it solved it in about a minute - whether his n-of-1 de novo, heterozygous single nucleotide mutation was likely passed down from mom or dad. It performed a read-backed phasing analysis on the data, identified a nearby SNP with overlapping coverage where mom was homozygous and dad was heterozygous. Identified my variant on his mutated allele so looks like it came from me..

It also crosschecked my data against AMCG Secondary Finding genes and ClinVar likely pathogenic/pathogenic variants and came back with identical results to my Natera Horizon carrier screening results.

I'd previously tried and failed to do this all with some ChatGPT guidance and subsequently hired a couple of bioinformatician post-docs at top tier universities via Upwork who had failed to give me satisfactory results.

And this is just getting started!

It's been a painstaking process of combing consolidator websites (eg. PetVet Care Centers, NVA) for practice names, verifying and adding them to a list over the course of over a year. I now get many people writing in to report practices that aren't on the list - admittedly it's not complete list as practices are still being acquired (although independents are now in the minority) and often the old practice branding is kept and the fact it's PE owned is hidden.

If anyone wants to see how private equity has transformed the veterinary industry check out www.privateequityvet.org/vet-list - over 7000 practices mapped across the US so far. Our dog died at the hands of a recently acquired PE practice :(

Wow, great work. This is the kind of citizen hackery we need in society :)