User:Barry Canton

Barry Canton Bio

2nd Year BE Grad Student working with Drew Endy.

• BE in Mechanical Engineering, University College Dublin 2002
• MEngSc in Mechanical Engineering, University College Dublin 2003

Communications

• PhD. Thesis Proposal
• File:BCwisconsin05.pdf

Projects

• Engineering the Chassis/System Interface
• Receiver Specification - Working with Ania Labno

Links

• Barry's Wiki - I can provide a username/password for this. Its where I keep my electronic lab notebook.

Random

• E. coli restriction-modification system

• Modeling

I'd like to see a centralized and standardized source of models for biological parts and devices. A good framework for this would be the registry of standard biological parts. Each part and device should have a simple ODE model of its behavior accompanying it. In fact, this registry of models would operate identically and confer all the same advantages as a registry of parts. Namely, it would produce simple standard models of parts that could be reliably and rapidly combined to form models of more complex devices. If everyone building models was drawing from the same pool of part models, we could be more sure that those models were reliable. Again, just as with the registry of physical parts, everytime I wanted to build a model, I wouldn't have to start from scratch, I could start from well tried parts.

For example a constitutive promoter has a model with no inputs (ignoring polymerase and sigma levels) and one output, PoPS. In Matlab, this would be a simple function with no inputs that returns a scalar output which is the PoPS output of the device -

PoPS_out = R0040;

A protein generator would have a model with a PoPS input and a protein production rate as output. For example -

dP = E0240(PoPS_in);

Note that E0240 might actually be a collection of part models for an RBS, coding region, and terminator -

function dp = E0240(PoPS_in)
RiPS = B0032(PoPS_in);
translation_rate = E0040(RiPS);
dp = B0015(translation_rate);

The part models for R0040 and E0240 could be put together in an obvious way to form a model of a reporter device.

We already have models for many of our simple parts that could be combined easily if only steady state conditions were considered. Some more organization would be required to allow each model to represent the time varying behavior of a device as combining devices would require the assembly of ODE's from different files. It should still be very possible though.