To the best of my knowledge, what you're looking for doesn't currently exist, but there are two open standards efforts that I'm involved in that are aiming to bring it into being.
1) SBOL best practices proposal for "Representation of Parts and Devices for Build Planning": this is a set of vocabulary and representations to describe a synthesis and assembly plan. https://github.com/SynBioDex/SEPs/blob/master/sep_055.md
2) PAML is a draft standard for a machine-independent protocol specifications. http://bioprotocols.org/ It currently supports export to Markdown for human execution and to Autoprotocol, and there are current efforts to support OpenTrons, and to map from SEP055 plans into PAML protocols.
In short: there's a group trying to put together the capability you're looking for as a free & open source community project, and if you're interested in contributing, more hands are welcome!
Thanks,
-Jake
On Friday, August 19, 2022 at 9:33:49 PM UTC-5 dank...@gmail.com wrote:
Thanks again Ravi Ramana
That was spot on helpful, Thanks 1e6 dude...
The way the entire assembly task is specified in machine readable form is what I wanted. That's is a wonderful negative example really.
Nearly a hundred CSV files mostly two columns of identifiers, then 9 base pair sets "deep in the heap". Starting with duplicating this completed project is months of work to just detangle those relations with iterated smashes of scary wet-lab. Assuming the goal is to vet the equipment, workflow and some science buried in those big ominous details....
Just because somebody else's computer understands a heap of files, does NOT mean any human does, so the transmission of know-how is negligible; ( but not completely absent. Depends on how many months you have ).
My presumption to improve such a thing is also pretty suspect in some regards. But that doesn't keep me from trying ...
As attached, X11 app for doing this with some semblance of rationality...
Reality is not created by gluing together 33K Excel files to make a fancy critter like you.
my ref: 17 Aug 2022, Toronto, NAFL, blogOn Wednesday, August 17, 2022 at 11:24:09 AM UTC-4 Nathan McCorkle wrote:Just search Google for genbank. You'll find plenty of files.On Tue, Aug 16, 2022, 3:16 PM Dan Kolis <dank...@gmail.com> wrote:Greetings,
I asked this on this blog earlier but maybe it god lost in threads of other issues at hand.
Of course its possible what I'm asking about doesn't really quite exist, and/or the question's just been disregarded.
Hmmm.
I'm hoping for a file or two that is used for submission to a machine or hybrid of piece of equipment and people to spec making a B.P. fragment, either/or DNA or RNA.The file ( ex. example ) maybe a URL for its definition. Im interested somewhat in more then just a string a nucleotides but what sort of metadata is closely coupled to the files design.
Any feedback is appreciated,
Dan Kolis
my ref: 16 Aug 2022, NAFL, blog, bio--
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