[Biococoa-dev] random thoughts

Koen van der Drift kvddrift at earthlink.net
Tue Jun 7 10:59:44 EDT 2005

Hi all,

Right now I am at a mass spec scientific meeting in San Antonio (www.asms.org), and just saw an impressive presentation about modified nucleotides in tRNA (characterized by mass spec). One thing I want to start working on when I am back is the introduction of modifications of BCSymbols. Not sure yet how to implement this, but a possibility could be to further subclass BCSymbol to a BCModification class. Each BCSymbol can then have a NSArray of BCModifications (which in turn can have modifications too). The modifications are then read from the data that is stored in BCFeatures.

In the airplane on my way to Texas I was sitting next to one of the pioneers of writing protein identification software through peptide mapping. He explained that one of the ways to speed up their algorithm was to use many threads. Not sure yet how the use of multiple threads will work in BioCocoa, but it might well be an approach to speed up algorithms that require a lot of calculations.

Another thing I recently though about is that the new class BCSecondaryStructure could be extended to DNA/RNA as well. 

let me know what you think on these issues.


- Koen.

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