Ed's Big Plans

Computing for Science and Awesome

Integrase Problem Introduction

without comments

In a meeting with iGemmers @ Waterloo today– specifically the Modeling team headed by Andre and supplemented by core members Sheena and John– a discussion was held on this year’s modeling project. We’re currently interested in creating a solver that will yield an arrangement of attX sites on a chasis bacterial host chromosome that can accomodate several rounds of deterministic recombination.

Plainly, we need to write software that will create a solution that is a sequence of DNA– this DNA is arranged such that specific sites that can be operated on by the enzyme integrase is sequenced so that it can accept several loops of artificial DNA to recombine with. In this design, we’re interested in a sequence for the host chasis, a sequence for the artificial loops and another loop for integrase to be produced at some arbitrary tonic level inside the cell.

The first step is to mathmatically formalize the problem– and along with it, some working particles of software that successfully model the problem space. The solver is a yet more abstract piece of software that will use these particles in its solution. This is similar to designing the notion of integers and arithmetic operators prior to using those components to solve algebra.

This description is very coarse– I’ll refine it in a later post after I’ve had some time to analyze the problem constraints and what software particles are important to set down on paper.

Eddie Ma

May 25th, 2009 at 12:35 am