Ed's Big Plans

Computing for Science and Awesome

Modeling Meeting

without comments

Modeling Team Selection with Flush();

Modeling Team Selection with Flush();

A modeling meeting occurred on Wednesday. Andre headed off the discussion and revisited the entire program layout in a nice chalkboard cartoon. Unfortunately, Andre generally doesn’t push down hard enough or make wide enough lines with the chalk in order to make a high enough contrast image against the black board for photography (i.e. faint drawing => no photos, sorry).

The discussion saw the formalization and division of the programming problem into three distinct software components as follows.

  • Genetic Fragment Operators
  • Genetic Fragment Filters
  • Overall Program Logic

Genetic Fragment Operators

These are the functions that represent reverse-complementation, enzyme activity etc..

Genetic Fragment Filters

These are functions that represent removing uninteresting, ‘inert’, undesirable and fatal fragments of DNA. This definition will become more precise once we’ve worked on the project a bit and better understand the philosophical correctness of each of these notions.

Overall Program Logic

The overall program logic will constitute producing some structure that represents a Big Bag of DNA (as opposed to a cell), communication between this Big Bag, the Operator module and the Filter module and of course– our main program loop.

What I’m doing…

I’ve been tasked with producing a universal representation of DNA which includes a circular iterator on a loop of DNA with an arbitrary starting position. This is OK to do in Python with the use of the ‘yield’ operator. I will be borrowing from Jordan / Brendan / My own previous ideas for this representation– we want to have an easy single-letter-token system and for the moment are happy with the single byte space ascii has to offer.

Eddie Ma

June 12th, 2009 at 8:41 am