The blog post at Synthetic Blogology covers what I've done today fairly well, http://igemcalgary.blogspot.com/2009/08/second-life-belated-update.html
In short: I completed the second part of the Biobricker I talked about last Friday, the portion of the code that actually assembles Biobricks together into devices. Remaining to do on the Biobricker is in world testing, and to tie up a few loose ends in the code.
I keep a little to do list of elements I would like to have done for the end of this iGEM season, specifically with the biobrick simulator:
- level_select
- home
- parts
- interaction_check
- biobricker
- cofactors for dna binding proteins
The level select will be one of the last to be finished, since choosing a level and using the parts provided by it will require most of the other features to be finished. The same goes with the Home screen, which will display basic information about the current level and serve as a launching point to the other tools available in the simulator. The Parts screen will let you create objects from an inventory of prebuilt devices, plus regulatory proteins and cofactors; I've already implemented an inventory like system in the Biobricker though, so this will be a copy and paste job.
The Biobricker and Interaction Checker are easily the most complicated remaining parts, so I'm working on them first! The Biobricker, as explained, permits assembly of custom devices in world. The Interaction Checker will scan your nearby DNA, proteins, and cofactors, looking for possible binding interactions between them. Basically, if it could happen, it should. This is a tool to prevent users from 'forgetting' the way a system actually would work in the current state, and may be used to determine whether you've understood the system enough to progress to the next level! The checker will be intelligent enough to detect whether a gene is on or off, and hopefully work intelligently with multiple copies of a single coding sequence in different activation states. Of course, the Interaction Checker won't be able to help as much with systems that have no steady state such as the Repressilator... there's always another valid interaction.
Last of all, I want to implement DNA binding proteins that can accept multiple cofactors, mostly so that I can have LacI behave approximately like the real thing with regards to Glucose, Lactose, and IPTG (but also TetR with Tetracycline, AtC). The implementation I have in mind is reprogrammable though, and has no upper bound on the number of cofactors per protein. So if you want to invent a monster with three allosteric inhibitors and five inducers, you'll be able to do it!
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