3 ms·

This looks really cool!! Are there similar tools or equipment available today? How does Serotiny compare to them in pricing, speed and effectiveness?

jfarlow 9y ago
We have a lot of friends building genetic design software. Each have slightly different focuses. Ours is primarily, and I think uniquely, focused on an abstraction above the DNA itself (protein construct design). We focus on biological function of the output of the DNA rather than the 'assembly code' of DNA itself. For better or worse, we're a 'C IDE' rather than an assembly editor. If you are skilled enough to read the genetic matrix, some of the other software permits more direct manipulation of DNA. Pinecone is useful if you need to work or communicate your designs at a higher level of abstraction. If you want cheap and dirty way to manipulate DNA, APE is great: http://biologylabs.utah.edu/jorgensen/wayned/ape/ http://biologylabs.utah.edu/jorgensen/wayned/ape/ And YC's own Benchling has fantastic web-based software for designing, sharing and keeping track of plasmids: https://benchling.com/ https://benchling.com/ Genome Compiler is impressive as well: http://www.genomecompiler.com/ http://www.genomecompiler.com/ SnapGene is another widely-liked native app for working with plasmid DNA: http://www.snapgene.com/ http://www.snapgene.com/ Pinecone chooses to focus on guiding designs in order to produce genetic tools that have particular functions rather than focusing on how to construct DNA. We leave the construction details to the DNA synthesizers. Pricing: design and individual use is free, we charge a percentage of the manufacturing cost for designs submitted through us. We also make money building custom infrastructure (of which Pinecone is an example) for companies needing to keep track and analyze their genetic designs at a functional level. Speed: The idea is because we use an abstraction above the DNA, certain kinds of high-throughput designs becomes VERY fast with Pinecone. "I want all proteins made with these 5 things up front, these 7 linkers, these 4 fluorescent probes - and all 140 combinations" - would take about 2 minutes to design with Pinecone, but would be days of error-prone work if done manually. Reliability: We can't guarantee novel designs will work - biology is hard. But we can help give novel designs the best chance of working. Pinecone showcases what has worked - and makes it easy to riff off of well-worn designs. And because you're buying de-novo synthesized DNA (not copy/pasting other's code), your sequences are exactly what you asked for, not just 'good enough'.
- theprop 9y ago
  I want to genetically engineer extremely intelligent mice...what tools should I use? Is this possible?
  - jfarlow 9y ago
    You still have to figure out what "intelligence" is, and how to transfer, manipulate, or otherwise encode for it. I don't think we have the tools to actually transplant intelligence yet. We are in the early stages of understanding it at all. The field of "optogenetics" https://en.wikipedia.org/wiki/Optogenetics https://en.wikipedia.org/wiki/Optogenetics has been a powerful genetic way to help start along that path to understanding how brains work, to what extent a mouse is intelligent, and how to affect neural processes.

jfarlow 9y ago

We have a lot of friends building genetic design software. Each have slightly different focuses. Ours is primarily, and I think uniquely, focused on an abstraction above the DNA itself (protein construct design). We focus on biological function of the output of the DNA rather than the 'assembly code' of DNA itself. For better or worse, we're a 'C IDE' rather than an assembly editor. If you are skilled enough to read the genetic matrix, some of the other software permits more direct manipulation of DNA. Pinecone is useful if you need to work or communicate your designs at a higher level of abstraction. If you want cheap and dirty way to manipulate DNA, APE is great: http://biologylabs.utah.edu/jorgensen/wayned/ape/ http://biologylabs.utah.edu/jorgensen/wayned/ape/ And YC's own Benchling has fantastic web-based software for designing, sharing and keeping track of plasmids: https://benchling.com/ https://benchling.com/ Genome Compiler is impressive as well: http://www.genomecompiler.com/ http://www.genomecompiler.com/ SnapGene is another widely-liked native app for working with plasmid DNA: http://www.snapgene.com/ http://www.snapgene.com/ Pinecone chooses to focus on guiding designs in order to produce genetic tools that have particular functions rather than focusing on how to construct DNA. We leave the construction details to the DNA synthesizers. Pricing: design and individual use is free, we charge a percentage of the manufacturing cost for designs submitted through us. We also make money building custom infrastructure (of which Pinecone is an example) for companies needing to keep track and analyze their genetic designs at a functional level. Speed: The idea is because we use an abstraction above the DNA, certain kinds of high-throughput designs becomes VERY fast with Pinecone. "I want all proteins made with these 5 things up front, these 7 linkers, these 4 fluorescent probes - and all 140 combinations" - would take about 2 minutes to design with Pinecone, but would be days of error-prone work if done manually. Reliability: We can't guarantee novel designs will work - biology is hard. But we can help give novel designs the best chance of working. Pinecone showcases what has worked - and makes it easy to riff off of well-worn designs. And because you're buying de-novo synthesized DNA (not copy/pasting other's code), your sequences are exactly what you asked for, not just 'good enough'.

theprop 9y ago
I want to genetically engineer extremely intelligent mice...what tools should I use? Is this possible?
- jfarlow 9y ago
  You still have to figure out what "intelligence" is, and how to transfer, manipulate, or otherwise encode for it. I don't think we have the tools to actually transplant intelligence yet. We are in the early stages of understanding it at all. The field of "optogenetics" https://en.wikipedia.org/wiki/Optogenetics https://en.wikipedia.org/wiki/Optogenetics has been a powerful genetic way to help start along that path to understanding how brains work, to what extent a mouse is intelligent, and how to affect neural processes.