James

cofounder @hoxbio | building integrated systems for discovery, health, and security

[James @basedsystems]

cool place

[James @basedsystems]

in kendall square for couple days

[James @basedsystems]

@Ginkgo @OmicsOmicsBlog @PharmaTechFocus @jrkelly sweet Jason

[James @basedsystems]

@netcapgirl who’s building this

[James @basedsystems]

@anshulkundaje I know a guy who figured out how to generate the structures dataset without crystals. So, there will be much larger datasets in a bit of time

[James @basedsystems]

putting this tweet on the wall in the office

[James @basedsystems]

downtown livermore feels a little like Palo Alto with shittier cars

[James @basedsystems]

@SashaGusevPosts will be a lot of this. probably need a way for centralized domain expertise to reach out to the datasets and pick at them live as like a service

[Blake Scholl 🛫 @bscholl]

If you're building real things—as an engineer, entrepreneur, technician—consider having more children earlier than you thought.

Your children will have the irreplaceable inspiring experience of growing up with parents who do things and make things. More👇

[James @basedsystems]

in the future the large companies will have been started in group chats

[Jon Erlichman @JonErlichman]

First offices of 6 companies worth a combined $21 trillion.

[undefined behavior @undebeha]

i think trump is working on some strange generalization of the collatz conjecture

[Jared Duker Lichtman @jdlichtman]

Update on Erdős Problem 1196:

In joint work, we refined and adapted the proof method from GPT-5.4 Pro to give proofs of several additional problems. This includes another 60 year old conjecture by Erdős, Sárközy, and Szemerédi.

A proof is valued not just by the problem it solves, but by what new avenues it opens up. This is perhaps one of the first examples of an AI-generated proof having downstream impacts, which we are still exploring.

We are announcing the result today at the Future of Mathematics Symposium (see links below)

[James @basedsystems]

when the kids are destroying the house but also leaving you alone so you gotta decide if you’re gonna get up and do something about it

[James @basedsystems]

@bazarovturg also, we rip apart how the standard software works because we need to optimize for correctness in our services. often you dig in and find missing knobs or broken / complex code

[James @basedsystems]

We wrote our own hyper-efficient version of the STAR aligner.

Typically it costs around $35 in cloud compute to process 30k cells with Cell Ranger. Ours costs so little that we don't charge for it. Also ours works with nanopore.

If you prefer pseudoalignments, then you can run it in pseudoalignment mode -- obviously we don't charge for that too.

All results instantly integrated with our other tools. As soon as a run finishes you can open alignments or expression matrices in our viewers without moving anything.

Let me know if you want to try it!

[James @basedsystems]

@bazarovturg we use it to run various internal services. better to just write a new, efficient one that integrates with the rest of our stuff

[James @basedsystems]

@wannabe_ary @chapmanb I’ll make sure we support pip-seq geometry

[James @basedsystems]

In entrepreneurship we call this “effectual reasoning”

[Doc Strangelove @DocStrangelove2]

Whoever said a shopping cart can't be used as shooting platform was in fact wrong.

[James @basedsystems]

@KiaNeu6 it’s something like 100x more efficient