[ If you find this randomly, this is a work in progress! -KG 6 Nov 2020 ]
This Keoni Gandall's DNA Toolkit git. This is where I design DNA toolkits. The DNA here isn't meant to be novel - it is meant to take the best of what other people have designed or created and organize it in a comprehensive and detailed way. For right now, I intend to design everything here by myself, so you can also have an consistent experience in reading about these toolkits.
The toolkits I'm writing up are based off of an idea I've had for a while - that DNA engineering is interconnected and contextual. This idea is expanded upon in the "BioFAB Human Practices" as the 3 context problems of synthetic biology - genetic context, host context, and environmental context. Briefly, genetic context is the local context of a genetic circuit - is it on a plasmid, or is it on the genome, or something else? Host context is the context of the host itself - is the host a bacteria? Is it a yeast? Environmental context is, as expected, environmental - is this circuit to be placed at 37c or 30c? These 3 contexts, and not controlling for them, make synthetic biology hard.
However, I believe that these 3 contexts can be automated away. I believe that there will be a time in which genetic context, host context, and perhaps even environmental context will be largely irrelevant to bioengineers. These toolkits are meant to assist us in transitioning to that new world.
How? All of these toolkits are being designed to allow for affordable automated construction of DNA, and will be shipped using the Sporenet protocol. If we can get enough people using the same toolkits (by making them high quality), affordable automation solutions can/will be built because there is a sufficient amount of people who want them to be built. Affordable automated construction can be combined with automated design software, allowing for far more testing and building. Automated solutions already exist in the world, but they are typically silo'd within institutions. I hope through careful design for automation and mass distribution we can have automation of genetic design, build, and test for the masses.
As an extension of the concept of automated construction, I aim to deemphasize the importance of individual parts, and instead aim to analyze each toolkit as a system of different relationships and purposes (inspired from "Thinking in Systems: A Primer"). There are 2 kinds of toolkits: Set toolkits and Atomic toolkits. Set toolkits are built for single goals - for example, you could have a yeast backbone toolkit, which can build yeast backbones. Atomic toolkits are built for single units - for example, a variety of yeast promoters. Atomic toolkits allow you to fine-tune constructs for particular contexts while Set toolkits enable you to build desired constructs in the first place.