jfarlow

11 ms·

61.
by jfarlow 8y ago
Yep - and because DNA's base pairing rules are so well-studied, so predictable, and information-carying, we can use DNA for its material properties in addition to or even separate from its genetic properties. In terms of software, Shaw
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by jfarlow 8y ago
We do this at Serotiny [1]. And others are working on this as well for different specific purposes. We use some very basic ML (the data is very sparse, wide, but any hit above a low baseline is very valuable). The curious part, from our
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by jfarlow 8y ago
Don't let it make you mad - this is science. And this kind of refining progress is precisely how science should work. This is a good thing. Start with a toehold, and move inward. Cycle back when you realize your toe wasn't i
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by jfarlow 8y ago
Serotiny | Bay Area, CA | Lead Back-End Engineer (First SWE Hire) | Full Time Serotiny is a synthetic biology design firm that invents custom proteins to cure cancers and genetic diseases. We help design proteins involved in CAR-T therapies
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by jfarlow 8y ago
I still remember when 'googol' was my 2nd grade answer to 'no, I like it thousands better, no millions better, no billions better, no googol better!' And somehow that silly abstraction for "a big number number than
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by jfarlow 8y ago
I am curious how much of this is a bioinformatics insight. If your dataset is looking under the lamp-post for coding sequences, then you'd be unlikely to pull out non-coding regions for analysis. However, if you're strictly empi
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by jfarlow 8y ago
Machinery of Life is a fantastic introduction to an intuition for what proteins and the mechanics of their scale. https://www.amazon.com/Machinery-Life-David-S-Goodsell/dp/03...
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by jfarlow 8y ago
That kind of thing is generally thought of as machine-learning, or AI assisted "Drug Discovery", but there's not a great name for the field at large. Because there are so many different kinds of 'medicine' at this
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by jfarlow 8y ago
It is our job at Serotiny. We take plain-language requests for proteins with novel functions (not just binds more tightly, or produces this enzymatic product over that one), and we use the catalog of existing natural protein components to
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by jfarlow 8y ago
https://www.spacexstats.xyz/
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by jfarlow 8y ago
Serotiny | Bay Area, CA | Lead Back-End Engineer (First SWE Hire) | Full Time Serotiny is a synthetic biology design firm that invents custom proteins to cure cancers and genetic diseases. We help design proteins involved in CAR-T therapies
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by jfarlow 8y ago
You're right! The paper itself is strongly agnostic to its analysis scale, while the Quanta article focuses entirely on DNA sequence. > Our embedded computational network architecture can be interpreted either at the levels of cell
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by jfarlow 8y ago
So, coming from the science side of things where we 'program' DNA in order to design genes not found in nature, it's clear evolution works at many scales simultaneously. And those scales each need to be accounted for in order
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by jfarlow 8y ago
Serotiny | Bay Area, CA | Lead Back-End Engineer (First Software Engineer Hire) | Full Time We're a recently funded synthetic biology company that has built the beginnings a biologically-aware API for designing novel genetic machines.
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by jfarlow 8y ago
- High level article [1] - A "Roadmap" from the semiconductor/data side, looking at DNA from its first principles [2] - Review combining the tech side with the bio side [3] [1] http://www.sciencemag.org/news&#
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by jfarlow 8y ago
Yes. Many orders of magnitude. However, if you're just doing cold storage, the data-density of DNA is many orders of magnitude greater. With essentially sub-nanometer 3D atomic data-density you can pack a staggering amount of data i
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by jfarlow 8y ago
This is already being deployed in therapies today - https://en.wikipedia.org/wiki/Checkpoint_inhibitor And it works well in conjunction with other therapies that guide or otherwise help the immune system find the cance
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by jfarlow 8y ago
Serotiny | Bay Area, CA | Lead Back-End Engineer (First Software Engineer Hire) | Full Time We're a recently funded synthetic biology company that has built the beginnings a biologically-aware API for designing novel genetic machines.
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by jfarlow 8y ago
Those "physical attributes" are most grossly characterized with those same measures- size, shape, length, stiffness, etc. And if you have access to those simple attributes you get a lot farther than if you just think about a g
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by jfarlow 8y ago
My email address is my first name at serotiny.bio -Justin
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by jfarlow 8y ago
Serotiny | Bay Area, CA | Lead Back-End Engineer (First Hire, full-time) We're a recently funded synthetic biology company that has built the beginnings a biologically-aware API for designing novel genetic machines. At Serotiny we inve
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by jfarlow 8y ago
I'd say, arguably, yes. And not necessarily because those examples use numeracy directly - but rather because a biological numeracy would provide a foundation to an intuition that would prevent the beginner's mistakes in those ex
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by jfarlow 8y ago
This is one of the most important parts of biological intuition that is very hard to get access to. Even PhD graduates often stumble when asked even about the order-of-magnitude of some of these values. It's not dissimilar to the ge
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by jfarlow 8y ago
Very fun. I put in some scientific proteins, and it spits out their common fluorescence staining colors: ZO1 (stain tight-junctions, often blue): https://picular.co/zo1 (see https://www.google.com/search?tbm
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by jfarlow 8y ago
Yep, that's because CARs are one of the first medically relevant genetic engineering projects that is not just a "cut-and-paste change". It is the insertion of a new capability into the immune cell. That is of a very di
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by jfarlow 8y ago
Serotiny | Back-End Engineer (First Hire, full-time) | Bay Area, CA We're a synthetic biology company that has built the beginnings a biologically-aware API for designing novel genetic machines. At Serotiny we invent proteins to cure c
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by jfarlow 8y ago
Serotiny | Back-End Engineer (First Hire, full-time) | Bay Area, CA We're a synthetic biology company that has built the beginnings a biologically-aware API for designing novel genetic machines. At Serotiny we invent proteins to cure
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by jfarlow 8y ago
It's been talked about a few times on HN already, but it's a very interesting protein. It suggests a genetic delivery mechanism that is already in the body - and thus doesn't invoke a lot of the immunogenic properties of usi
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by jfarlow 8y ago
This is a great project for a specific kind of problem - and one that's not the common target for silicon valley. It's hard to get good and useful data in places where connectivity is low. And the (coding and social) logistics of
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by jfarlow 8y ago
For those interested in seeing Glenda: https://blog.golang.org/gopher

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