Ed's Big Plans

Computing for Science and Awesome

Operator Group Meeting

without comments

The Operator Group (UWiGem/Modeling/Operators) had a meeting about a week ago– the meeting ended up being between three people: Matthew, Andre and me at the iGem office. We’ve basically figured out everything we needed to in terms of raw interfaces between our module and the remaining two modules (Filtering Group and Giant Scaffold Group). The DNAClass was updated with the needs Andre presented– one of which is the ability to iterate over a DNAObject while returning yielding both the token index and token in a duplet: (index, token).

The implementation of the enumerate() built-in in Python (PEP 279) doesn’t allow for abstract function overriding. It always counts a collection as it iterates over it starting from zero. Ideally, the count should reflect the index of the circular DNA strand which means that it should be able to count forward or backward (iterate as reverse compliment), and count from any arbitrary position in the loop.

Note that the reverse compliment copy constructor (DNAObject.rc()) does not cause indexes to be reversed… It actually produces a reverse compliment strand and doesn’t do anything special with the indices (i.e. The new strand increments positively as it iterates forwardly). This behaviour is being debated now– On the one hand, it’s correct because a reverse compliment strand is a new strand; however, it is not a strand de novo– it came from a positive sequence.

I’m now waiting for Andre to let me know about the functions and data frameworks needed for the Operators module; my feeling is that the functions will be the straight forward integrase enzyme actions and that the data framework will simply be a python list.

Eddie Ma

June 26th, 2009 at 2:42 pm