[DIYbio] Re: Files for DNA / RNA creation via automation - oh wow

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

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