CS151: Computer Programming Fundamentals with C++
I work at the intersection of computer science and molecular cell biology. Using machine learning techniques I discover the structure of cell signalling networks. Understanding cell signalling networks helps me understand the computational machinery of living cells.
Quantifying the Effect of Colony Size and Food Distribution on Harvester Ant Foraging, Tatiana P. Flanagan, Kenneth Letendre, William R. Burnside, G. Matthew Fricke, and Melanie E. Moses, PLoS ONE, 2012.
GetBonNie for building, analyzing, and sharing rule-based models, Bin Hu; G. Matthew Fricke; James R. Faeder; Richard G. Posner; William S. Hlavacek Bioinformatics 2009; doi: 10.1093/bioinformatics/btp173 published by Oxford Journals
BioNetGen: Biochemical reaction networks are central to understanding and influencing the operation of biological cells. GetBonNie (http://getbonnie.org) and BioNetGen (http://www.bionetgen.org) automate the development of reaction networks so that biologists can create and study detailed models of cellular biochemistry. Poster. Video.You can download the software here: OS X, Windows. Be warned however that these distributions are of RuleBuilder 1.50 Beta bundled with BioNetGen 2.0.28, which are out of date. For the latest builds please go to the bionetgen website.
Receptor aggregation by intermembrane interactions: A Monte Carlo study
We model proteins on the cell surface with a Metropolis Monte Carlo lattice and measure the conditions under which clustering occurs. We then bring two virtual cell membranes into contact and measure the cross membrane binding forces needed to cause protein phase separation. Paper in Biophysical Chemistry. PowerPoint Web Slideshow. PDF Slideshow.
KomPhy: Algorithms for reconstructing phylogenies from character sequences encounter enormous search spaces even for small numbers of taxa. Techniques are needed to speed up the exploration of these spaces so that larger problems can be approached. In the past neural networks have provided a framework for tackling complex problems very quickly. My thesis describes and tests a new neural network approach to phylogenetic reconstruction called KomPhy. Thesis. Slideshow. Software.
CultureAL: Semester project for David Ackley's Artificial Life course at UNM. CulturAL uses a very simple framework to explore the interaction of learned traits (directly and through peer emulation) and biological traits. Processes such as 'shielding' and the Baldwin Effect are explored. Learning in this model benefits the population as a whole through emulation but is counterproductive for the learner who is much better off copying others and procreating. The population as a whole evolved to minimize direct learning and maximize emulation of peers relying on the background mutation rate to produce enough 'learners' to feed the emulation strategy.. The most prevalent impact shared knowledge has on genetic evolution is shielding, which allows populations to survive that would otherwise die out and allows genetic mutation to explore the fitness landscape with more freedom. Presentation.
Madcat: Extension of the Copycat AI framework to a robotic path finding problem which formed the basis of Joseph Lewis' PhD. Starcat is Joseph's current research. Madcat NASA Student Conference Paper.
My wife, Suzanne, and I have four boys: Henry, Leo, Owen, and Tristan. We live in Albuquerque, New Mexico, USA. I was born and raised in Shrewsbury, UK, but have lived in Mount Airy, North Carolina and Albuquerque, New Mexico for most of my life. I have been obsessed with computers since playing with Commodore 64 when I was ten years old.
Go Figure Software is my contracting company. Through Go Figure Software I have provided programming services to scientists at the UNM Physics Department and Los Alamos National Labs.
Mt. St. Helens, Oregon
San Deigo, California
Yr Wyddfa (Snowdon) and Anglesey, Wales
Charles Darwin's Childhood Home