Files for DNA / RNA creation via automation

[Dan Kolis]

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

[Brian Caplin]

Buy an old synthesizer..couple hundred bucks..just make sure it comes with software.. that'll have what ya need..fluid flow volumes.. incubation times..etc.

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[Ravi Ramana]

Maybe this helps

https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT/tree/oup_synbio

https://academic.oup.com/synbio/article/5/1/ysaa010/5869449

It gives the whole assembly instructions (hybrid) for DNA. 

[Nathan McCorkle]

Just search Google for genbank. You'll find plenty of files.

[Dan Kolis]

Yes ! very helpful thank you.

Regs,

Dan

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/d777798d-2175-4ccf-9e01-f7437d1694ean%40googlegroups.com.

[Dan Kolis]

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, blog

[Jacob Beal]

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

[Dan Kolis]

Thank you Jake.

My proposal which has morphed into a running IDE ( predictably, a X11 App in Python3 ) seems like it co-exists unusually well with a number of Synthetic Biology software integration projects. Thank you for your message, it was VERY helpful nearly immediately. I had no difficulty in getting accredited for Google group BioProtocols and have been reading the supplied materials over the last 2 hours...

Here is the abstract of a primary document I wrote about the centroid of my interests:

The creation of a computer-script language named Nucleotide Assembly Functional Lan-
guage (NAFL) attempts to achieve two objectives: Firstly, improve the scope of FASTA
searches by making them more generalized and include non-Central Dogma atomic
elements correctly. Secondly, host the modelling of many life science programmes in
new Synthetic Biology with less or no custom programming.

The amount of sequence, sequence-like and ancillary information when working through
a specific life science problem is immense. NAFL supports metadata that follows com-
puter queries and modelling as work proceeds automatically. This is particularly relevant
in the frequent case where work sessions span multiple sittings and intermediate re-
sults are shared over time and space with multiple workers. FASTA and sequences of
nucleotide and gene-like sequences are the most prominent organisational elements
in the code’s Integrated Design Environment around NAFL. Improving the interac-
tion of searches executed for DNA, RNA and proteins against databases has direct
utility; but this new nomenclature in machine readable form also avoids changing
programs to understand returned sequence matches. The computer dialog focuses on
the user experience and avoids repeating similar steps with slightly different criteria
by representing lists of project components as opposed to working through one at a
time sequentially. The subsidiary tasks for many tasks like protein folding and mRNA
planning is supported with similar syntax human-machine dialog.

NAFL is constructed from first principles to be uniform across computing platforms;
Enabling the execution of stored scripts on personal, cloud and cluster configurations
interchangeably in any common operating system. A goal is to move the user experience
into direct real-time encounters with problems and solutions. In contrast, the usual
creation of endless database flat files and maintenance of notes is seen as an old world
practice. Instead, NAFL substitutes interactivity and automates much note-taking. Since
sizable delays do occur, NAFL specifically implements asynchronous human-machine
interactions; Instead of waiting many works-in-process results are returned out of order
as partial solutions evolve.

Back to your helpful message; ( thank you again ! )

SBOL(3) is useful for some sorts of improvements of sequence BP management to outcomes, I've carefully pulled apart a vast whole cell simulation by a bunch of workers in the shadows of Venter... Maybe 2/3 of the 40 models inside as motifs of simulation are imported as SBOL.

This is that project, its pretty remarkable really:
  https://www.cell.com/action/showPdf?pii=S0092-8674%2821%2901488-4

Jake said:
" 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. "

Dan continues:

I work on the IDE which barely even addresses the notion I propose. I am so invested in a non-batch processing, real-time s/w for Base Pairs the deeper notion is still barely touched.

I tell people: "Im trying to write a masterpiece"....

If any ideas occur to you about the NAFL language notion, lets poke some chars into this pipeline here !

I toy with the idea of rebuilding this work into a real IDE so Venters DIY-cell could be start, stopped, etc like a program in a debugger. This article points ot more formal papers, etc. This was written 100% ass-of-fire any old way to get it to work for show and tell. That's just wonderful, but its not orderly enough to use too directly. Its rough nature proves the point its possible, a serious milestone achieved.
  https://www.cell.com/action/showPdf?pii=S0092-8674%2821%2901488-4

I think on a few computers together it could simulate a single Venter cell at 10 times real time.

Regards,
Dan Kolis

my ref: nafl,  blogs, 22 Aug 2022, jake101