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libbiosyntax, a C reimplementation of bioSyntax #70
Description
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:
- biosyntax.h
- biosyntax.c
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
Activity
kojix2 commentedon Jun 15, 2026
Ruby bindings: https://github.com/kojix2/ruby-biosyntax
ababaian commentedon Jun 30, 2026
Hey This is great, if you want to release it by MIT then feel free to do so. Also if you want to add a link/documentation of this to the biosyntax repo the please do open a PR and we can refer users to the C libraries as well.
kojix2 commentedon Jul 31, 2026
Thank you for your reply, @ababaian. Are you the current owner or maintainer of the bioSyntax project?
I would be happy if libbiosyntax could use the MIT License. However, because I used the original source code as a reference, I believe I should follow the GPL license chosen by the original authors.
If it could at least be relicensed under the LGPL, it would be much easier to use from language bindings. Applications could then link to the shared library without using the same license.
ababaian commentedon Aug 19, 2026
I am the current owner and maintainer yes. I hereby decree official allowance of kojix2 to make a derivative of the biosyntax codebase for C to be released under the MIT license.
kojix2 commentedon Aug 20, 2026
@ababaian
Sorry, but I’m having trouble understanding your reply. What exactly are you decrying?
Reading it straightforwardly, it sounds as though you may have misunderstood me as saying that I changed the license. However, libbiosyntax, ruby-biosyntax and pybiosyntax are still distributed under the GNU General Public License v3.0. I have not changed the license. In the first place, I cannot change the license without permission.
What I proposed was whether you would be willing to allow LGPL. You suggested changing it to MIT, and I replied that I would be happy if MIT were possible.
Or did you mean “declare/decree” rather than “decry”? I’m not a native English speaker and rely on machine translation for this conversation, so I can’t tell whether it was a typo or whether I was actually being criticized.
ababaian commentedon Sep 1, 2026
Sorry I was just trying to sound funny by being overly formal but did end up using the wrong word. I'll all LGPL yes. Go for the C library.
kojix2 commentedon Sep 4, 2026
Thank you.
I plan to formally relicense libbiosyntax under LGPL-2.1-or-later, and release the language bindings under the MIT License.
Please let me know if you see any issue with this arrangement.
I appreciate your permission and your help with this.
Relicense libbiosyntax under LGPL-2.1-or-later