Cap'n Proto VS poly

Yeah I pretty much only use my own alternate container implementations (from KJ[0]), which avoid these footguns, but the result is everyone complains our project is written in Kenton-Language rather than C++ and there's no Stack Overflow for it and we can't hire engineers who know how to write it... oops.

[0] https://github.com/capnproto/capnproto/blob/v2/kjdoc/tour.md

- may massively reduce the latency involved.

Those sharing Cap'n Proto-encoded data may have particular interest. Cap'n Proto (https://capnproto.org) is fantastic at its core task - in-place serialization with zero-copy - and we wanted to make the IPC (inter-process communication) involving capnp-serialized messages be zero-copy, end-to-end.

That said, we paid equal attention to other varieties of payload; it's not limited to capnp-encoded messages. For example there is painless (<-- I hope!) zero-copy transmission of arbitrary combinations of STL-compliant native C++ data structures.

To help determine whether Flow-IPC is relevant to you we wrote an intro blog post. It works through an example, summarizes the available features, and has some performance results. https://www.linode.com/blog/open-source/flow-ipc-introductio...

Of course there's nothing wrong with going straight to the GitHub link and getting into the README and docs.

Currently Flow-IPC is for Linux. (macOS/ARM64 and Windows support could follow soon, depending on demand/contributions.)

FWIW, my C++ toolkit library, KJ, does the same thing.[0]

But presumably you could still write a condition predicate which looks at things which aren't actually part of the mutex-wrapped structure? Or does is the Rust type system able to enforce that the callback can only consider the mutex-wrapped value and values that are constant over the lifetime of the wait? (You need the latter e.g. if you are waiting for the mutex-wrapped value to compare equal to some local variable...)

[0] https://github.com/capnproto/capnproto/blob/e6ad6f919aeb381b...

The second one is to encode data in such a way that you can read it and operate on it directly from the buffer. You write data in a layout that is the same, or easily transformed as types in memory. To do that you usually need to encode with a known schema, only Sized types to efficiently compute fields locations as offsets in the buffer, and you usually represent pointers as offset into the encode. You can look at capnproto protocol for instance https://capnproto.org/

Worked well for Cap'n Proto (the cerealization protocol)! https://capnproto.org/

With all due respect, you read completely wrong.

* The very first use case for which Cap'n Proto was designed was to be the protocol that Sandstorm.io used to talk between sandbox and supervisor -- an explicitly adversarial security scenario.

* The documentation explicitly calls out how implementations should manage resource exhaustion problems like deep recursion depth (stack overflow risk).

* The implementation has been fuzz-tested multiple ways, including as part of Google's oss-fuzz.

* When there are security bugs, I issue advisories like this:

https://github.com/capnproto/capnproto/tree/v2/security-advi...

* The primary aim of the entire project is to be a Capability-Based Security RPC protocol.

I like how they use capability-based security [0] and use Cap'n Proto protocol. This is another technology that is slow to get broad adoption, but has many things going for when compared to e.g. Protocol Buffers (Cap'n Proto is created by the primary author of Protobuf v2, Kenton Varda).

[0] https://sandstorm.io/how-it-works#capabilities

[1] https://capnproto.org

Related but not Rust-specific: FlatBuffers, Cap'n Proto.

- 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)