GIL Devlog 1: Version 0.2

Hey everyone! Welcome to the first GIL devlog! This past week, I’ve been working to finish version 0.2 of GIL. I’ve got several exciting bits of news about this coming version, but first I should give a bit of an explanation as to what exactly GIL is.

To be honest, I don’t exactly know what GIL is. Right now, I’ll go with what I wrote on the GitHub page. GIL is a collection of tools designed to simplify synthetic biology. While that might not be completely true after some of the changes I’ve got planned for version 0.3, it is true right now. Furthermore, GIL is open source. GIL is licensed under the GNU GPL-3.0 license. This means that you can do anything with the source code, you can even take it and sell it, but you have to license whatever you do with it under the same license.

Finally, here’s what’s new with version 0.2. First, I’ve changed what kind of file GIL outputs. In version 0.1, GIL would just output a string of bases with no context whatsoever. This is fine if you’re only working on one protein, but it becomes a problem if you want to design anything more complex. In this version, GIL outputs a GenBank .gb file. This lets you directly import compiled sequences into something like Benchling, and it lets you specify features and different proteins using

#region region name

and

#endRegion

An even more important change is the support for more organisms introduced in GIL 0.2. Version 0.1 only supported baker’s yeast, but version 0.2 introduces support for Pichia Pastoris and E. Coli. This took about half an hour to do, so I’m going to be including at least a couple of new targets with every upcoming release. Finally, I’ve added a new keyword. The From keyword translates DNA from one supported organism to the target. Here’s an example of its use:

#target E.coli
From Yeast
{
    //Some genetic sequence
}

Finally, I’ve changed %AminoSequence to AminoSequence to make things less complicated. When I publish this version 0.2 should already be live, so if this sounds interesting you should check out the GitHub repository here. With all that said, see you next week.