Hello bioSyntax team,
I hope someone is still reading this in 2026.
Yesterday, I created a project called libbiosyntax:
https://github.com/kojix2/libbiosyntax
It is a small C library that reimplements bioSyntax.
I developed libbiosyntax with the help of Codex through an iterative process. My main contribution was deciding that the bioSyntax idea was worth porting to a small C library, then spending a weekend reviewing, testing, and repeatedly guiding the AI-assisted implementation until it reached its current form.
This is not a clean-room implementation. I used the original bioSyntax source code as reference files. For that reason, I released libbiosyntax under GPL-3.0 in order to respect the original license.
The library consists of two files:
If someone wants to use it from C, they can simply copy these files into their project. For use from Python or other languages, bindings can be written around the library.
I know this is different from writing the whole library by hand, and I do not want to overstate my contribution. But I felt the bioSyntax idea was worth preserving and adapting into a small C library.
To be honest, I would like to release libbiosyntax under LGPL instead of GPL-3.0, if that is acceptable to the original bioSyntax authors.
I fully respect the current GPL-3.0 license. However, for a small embeddable C library, LGPL would be much easier to use in practice, especially in bioinformatics projects that are already MIT-, BSD-, or Apache-licensed.
I think the idea behind bioSyntax is excellent, and I hope libbiosyntax may help make it useful in a few more contexts.
Have a nice day.
kojix2
Hello bioSyntax team,
I hope someone is still reading this in 2026.
Yesterday, I created a project called libbiosyntax:
https://github.com/kojix2/libbiosyntax
It is a small C library that reimplements bioSyntax.
I developed libbiosyntax with the help of Codex through an iterative process. My main contribution was deciding that the bioSyntax idea was worth porting to a small C library, then spending a weekend reviewing, testing, and repeatedly guiding the AI-assisted implementation until it reached its current form.
This is not a clean-room implementation. I used the original bioSyntax source code as reference files. For that reason, I released libbiosyntax under GPL-3.0 in order to respect the original license.
The library consists of two files:
If someone wants to use it from C, they can simply copy these files into their project. For use from Python or other languages, bindings can be written around the library.
I know this is different from writing the whole library by hand, and I do not want to overstate my contribution. But I felt the bioSyntax idea was worth preserving and adapting into a small C library.
To be honest, I would like to release libbiosyntax under LGPL instead of GPL-3.0, if that is acceptable to the original bioSyntax authors.
I fully respect the current GPL-3.0 license. However, for a small embeddable C library, LGPL would be much easier to use in practice, especially in bioinformatics projects that are already MIT-, BSD-, or Apache-licensed.
I think the idea behind bioSyntax is excellent, and I hope libbiosyntax may help make it useful in a few more contexts.
Have a nice day.
kojix2