poly VS concise-encoding

- https://github.com/TimothyStiles/poly: Poly is a fast, well tested Go package for engineering organisms.

Poly: Fast Go package for engineering organisms

You might want to look at computational biology. Jim Allison won the Nobel Prize back in 2018 for his work on immunotherapy for cancer and there's a lot of basic research work to be done to perfect this approach. Epigenetic clocks are really interesting too (see Steve Horvath's work). Also, there's synthetic biology, where you could, for example, explore this package that's written in Go: https://github.com/TimothyStiles/poly

Check out poly. It’s written in go and I’m using it for one of my projects too. The goal is that we should have high performance libraries that we can use knowing what people are working on the forks will give the community a leg up.

The most popular bioinformatic package I've seen in go is poly.

I write synthetic biology software for a living and maintain this open source, Go package for engineering DNA that has high test coverage and a nice little dev community around it.

https://github.com/TimothyStiles/poly

A large part of my project's community are devs that want to get into the field but can't tolerate the ridiculously low pay, laughably bad management, disrespect, and what amounts to 40+ years of technical debt that's endemic to biotech software.

I've had companies here in the Bay Area offer me 100K a year with a straight face. I've had companies during interview tell me they're looking for someone to help, "set up GitHub". I've seen job listings for low paid web dev positions require applicants to have PhDs.

The reality is that except for a growing handful of places management straight up won't know the difference between IT and software engineers. It's what I call the naive buyers problem.

The demand for software engineers in biotech is generated by naive buyers that don't know what they need, why they need it, or how to get it.

Benchling and Recursion Pharmaceuticals have reputations in the industry of paying, "standard software salaries". So do the research divisions at places like deepmind/microsoft/google but in my experience there's even new multi-billion dollar institutes where senior management has never even heard the term devops.

Most places advertise for "data scientist", positions or some analog, instead of software engineers. This is mostly because upper management has never met an actual practicing software engineer in a professional setting. Many come from academia where the culture and work requirements heavily disincentivize standard software engineering practices.

It's also not uncommon for a biotech company to either have a very under qualified CTO whose main programming experience is what they learned doing ML research like stuff during their PhD or not even have one at all which has huge downstream consequences.

This week a software engineer trying to make the switch to biotech actually DM'd me to ask why they were seeing a ton of data science / ML job positions but no software engineering / devops positions.

They were worried that these companies were trying to save on costs by forcing their data scientists to create infrastructure but it's actually worse than that. Most of these companies aren't even aware that there's supposed to be infrastructure.

Despite all of this the future is looking better and I'm starting to find new companies and positions that are well... reasonable. I learned about this thread from a friend at a party last night that works at one of these companies. There's a small, strong new wave of companies and developers out there pushing biotech software forward. Hopefully some (including myself) make it big while pushing the idea that better tech equals better biotech.

It is more like the X Y Z W. However, the X Y Z W bits I am working on as well (https://github.com/TimothyStiles/poly , https://github.com/TimothyStiles/allbase , trilo.bio, freegenes.org). Going for fully automated "make bacterium X produce molecule Y", but still a while away (but surprisingly not THAT far off)

"Local time" is time zone metadata. I've written a fair bit about timekeeping, because the context of what you're capturing becomes very important: https://github.com/kstenerud/concise-encoding/blob/master/ce...

This is basically why I ended up rolling my own text date format for Concise Encoding: https://github.com/kstenerud/concise-encoding/blob/master/ct...

ISO 8601 and RFC 3339 are fine for dates in the past, but they're not great as a general time format.

This looks similar to https://concise-encoding.org/

Dogma was developed as a consequence of trying to describe Concise Binary Encoding. The CBE spec used to look like the preserves binary spec, full of hex values, tables and various ad-hoc illustrations: https://preserves.dev/preserves-binary.html

Now the CBE formal description looks like this: https://github.com/kstenerud/concise-encoding/blob/master/cb...

And the regular documentation looks like this: https://github.com/kstenerud/concise-encoding/blob/master/cb...

Dogma also does text formats (Concise Encoding has a text and binary format, so I needed a metalanguage that could do both in order to make it less jarring for a reader):

https://github.com/kstenerud/concise-encoding/blob/master/ct...

https://github.com/kstenerud/concise-encoding/blob/master/ct...

Hey thanks for taking the time to critique!

I actually do have an ANTLR file that is about 90% of the way there ( https://github.com/kstenerud/concise-encoding/tree/master/an... ), so I could use those as a basis...

One thing I'm not sure about is how to define a BNF rule that says for example: "An identifier is a series of characters from unicode categories Cf, L, M, N, and these specific symbol characters". BNF feels very ASCII-centric...

It's still in the prerelease stage, but v1 will be released later this year. I'm mostly getting hits from China since they tend to be a lot more worried about security. I expect the rest of the world to catch on to the gaping security holes of JSON and friends in the next few years as the more sophisticated actors start taking advantage of them. For example https://github.com/kstenerud/concise-encoding/blob/master/ce...

There are still a few things to do:

- Update enctool (https://github.com/kstenerud/enctool) to integrate https://cuelang.org so that there's at least a command line schema validator for CE.

- Update the grammar file (https://github.com/kstenerud/concise-encoding/tree/master/an...) because it's a bit out of date.

- Revamp the compliance tests to be themselves written in Concise Encoding (for example https://github.com/kstenerud/go-concise-encoding/blob/master... but I'll be simplifying the format some more). That way, we can run the same tests on all CE implementations instead of everyone coming up with their own. I'll move the test definitions to their own repo when they're done and then you can just submodule it.

I'm thinking that they should look more like:

    c1

Ugh Unicode has been the bane of my existence trying to write a text format spec. I started by trying to forbid certain characters to keep files editable and avoid Unicode rendering exploits (like hiding text, or making structured text behave differently than it looks), but in the end it became so much like herding cats that I had to just settle on https://github.com/kstenerud/concise-encoding/blob/master/ct...

Basically allow everything except some separators, most control chars, and some lookalike characters (which have to be updated as more characters are added to Unicode). It's not as clean as I'd like, but it's at least manageable this way.

You might get a kick out of Concise Encoding then (shameless plug). It focuses on security and consistency of behavior.

https://concise-encoding.org/

In particular:

* How to deal with unrepresentable values: https://github.com/kstenerud/concise-encoding/blob/master/ce...

* Mandatory limits and security considerations: https://github.com/kstenerud/concise-encoding/blob/master/ce...

* Consistent error classification and processing: https://github.com/kstenerud/concise-encoding/blob/master/ce...

In the above example, `&a:` means mark the next object and give it symbolic identifier "a". `$a` means look up the reference to symbolic identifier "a". So this is a map whose "recusive link" key is a pointer to the map itself. How this data is represented internally by the receiver of such a document (a table, a struct, etc) is up to the implementation.

> - Time zones: ASN.1 supports ISO 8601 time types, including specification of local or UTC time.

Yes, this is the major failing of ISO 8601: They don't have true time zones. It only uses UTC offsets, which are a bad idea for so many reasons. https://github.com/kstenerud/concise-encoding/blob/master/ce...

> - Bin + txt: Again, I'm unclear on what you mean here, but ASN.1 has both binary and text-based encodings

Ah cool, didn't know about those.

> - Versioned: Also a little unclear to me

The intent is to specify the exact document formatting that the decoder can expect. For example we could in theory decide make CBE version 2 a bit-oriented format instead of byte-oriented in order to save space at the cost of processing time. It would be completely unreadable to a CBE 1 decoder, but since the document starts with 0x83 0x02 instead of 0x83 0x01, a CBE 1 decoder would say "I can't decode this" and a CBE 2 decoder would say "I can decode this".

With documents versioned to the spec, we can change even the fundamental structure of the format to deal with ANYTHING that might come up in future. Maybe a new security flaw in CBE 1 is discovered. Maybe a new data type becomes so popular that it would be crazy not to include it, etc. This avoids polluting the simpler encodings with deprecated types and bloating the format.