Gene Network Dynamics

As part of a collaboration between Dr. Bruce Edgar of the Fred Hutchinson Cancer Research Center, and Dr. Kerry Kim and myself at the CCD, we modeled the endocycle control circuit in Drosophila. The endocycle is a modified mitotic cycle in which cells replicate, and thus increase their DNA, but do not divide. Cells thereby become larger and achieve a higher metabolic output as the higher ploidy leads to increased rates of transcription and higher protein levels. We explored the endocycle's intrinsic tuner involving kinetic parameters that control its frequency. I developed Mathematica software to analyze and visualize the high dimensional parameter space of the network.

Visualization of Robustness Visualization of Path between two parameter sets Network viewer

Visualization of Robustness

Visualization of path in high dimensional parameter space between two good parameter sets

Network dynamics viewer


Data Distributing Technique

As many of the simulations at the CCD require enormous computational resources it is desirable that they be able to be run in parallel. In practice, writing a simulation to run in parallel can be quite challenging, as some tasks do not lend themselves easily to it. Assuming it can be partitioned properly the simulation will go faster when it is distributed amongst many computers, however, the speed at which an individual computer can get the next data segment it needs can be such a bottleneck to the overall performance that the advantages of going parallel are lost. My first project involved designing and writing a slick mechanism for distributing the data to exploit the benefits of parallel processing, by minimizing the hindering effects of the data bottleneck. The heart of this mechanism is a multicast network that cleverly polices the traffic between computers. One computer acts to synchronize the behavior of all others, via polling and handling requests loaded in a queue. Individual computers act as computational nodes on the network, listening for data they need, modifying it appropriately, and then multicasting it back onto the network, when permission is given by the synchronizing computer. The end result is the data "hovers" around the network, without needing to be gathered and resent redundantly between the computational nodes. This scheme increases the efficiency of the data flow, reduces the collisions between packets, and has scalability.

Mulicast network schematic

Multicast network schematic



Page written by Ryan Gile