Ed's Big Plans

Computing for Science and Awesome

Big Bang Day! A Recombinatron Story

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Matthew also has a post about Recombinatron & Big Bang Day here.

Integrase Enzyme Alphabet

‘Big Bang Day’ was this awesome Saturday morning where a bunch of the UWiGEM modeling folks came together and integrated our modules together. We ended up delegating more work, understanding the problem better and fixing up some of the logic in the big picture. After everyone had filed in and we managed to figure out how to synchronize with the SVN…. and after I managed to break the SVN and fix it again (thankfully!), it was time to get to work. I think the project as it stands right now is more or less done unless Giant Scaffold manages to find something that needs fixing.

Big Picture Drawn on the Chalk Board

The big picture was simplified to three giant objects that passes a big bag of DNA to one another in sequence.

The DNA bag is actually a list of DNAClass Objects (DNAObjects)– We decided not to create our own collection… there’s already a Python list. The Giant Scaffold module controls the movement of the DNA bag or subset there of from storage to Operators to Filters.

I was working with the Operators team– Basically, Matthew finished our team’s work because I managed to get swamped with thesis defense preparations, and Andre managed to take down the UWiGEM server.

(Andre incidentally has a post about taking down servers and making backups here.)

The Operators team ended up producing two big functions (and their little internal functions) and one support function.

A Couple of Filters

reactOneStrand(DNAObject) – Produces a list of resultant DNAObjects when the integrase enzyme is used on a single strand of DNA– this function may produce a one-list, two-list or three-list of DNAObjects. One-lists result from inversion (indirect) reactions, two-lists result from excision (direct) reactions, and three-lists result from palindromic operators.

reactTwoStrands(DNAObject, DNAOther) – Produces a list of resultant DNAObjects when two strands of DNA are reacted together with integrase.

The Filters team split their filters into three big enclosing functions– these three functions are equivalent to categories based on the likelihood that a given event would happen in a cell (Frequent, Moderate, Infrequent).

I unfortunately had to leave roughly 2.5 hours into Big Bang Day on other business but was happy to continue the madness online and on a subsequent Monday.

And now… some more photos…

Look! Everyone’s on their laptops– gee, I didn’t know they had Python on computers now!

Wylee, Bradon, Jordan

Wylee, Brandon and Jordan are all part of the Filters team.

Chong, Mattew, Andre

Chong is part of the Giant Scaffold team. Matthew and Andre are part of the Operators team.

Eddie Ma

July 3rd, 2009 at 1:12 pm