Bioinformatics

Making Pretty Pictures I started to learn to program about 5 years ago running population ecology models in mathematica . Yesterday, I found an old mma notebook with a model modified to include differential parasitoid dispersal to adjacent host cells depending on the host density in those cells. It's bascially a discrete-time Nicholson-Bailey model . But in a grid of cells, where each cell contains a population of hosts (H) and parasitoids (P) that give birth, die, eat, and get eaten according to the NB model. Each generation, following birth/reproduction/predation, the hosts and parasitoids disperse. The hosts disperse equally to the 8 surrounding cells in their neigbhorhood. The parasitoids can move irrespective of host densities when the aggregation parameter (eta) is 0. When aggregation is 1 (eta == 1), the parasitoids move to adjacent cells in exact proportion to host densities in each of the surrounding cells. muH and muP (i'm too lazy to figure out how to write the symb...

My computer spends a lot of time looking for neighbors of a given location-- even more so for bio, than for geo. This is what I've learned about the options for doing smarter search so far. SELECT * from ( (SELECT * FROM ((SELECT * FROM feature WHERE start = ? ORDER BY start LIMIT 1)) as u) UNION (SELECT * FROM ((SELECT * FROM feature where stop = ? ORDER BY stop LIMIT 1)) as v) ) as w ORDER BY ABS((start + stop)/2 - ?) LIMIT 1 if you fill in ? with an integer location, that query will return the closest feature most of the time. It's verbose if not ugly, and that's only for 1 dimension. It can return the wrong feature in certain cases.... You have to write it like that in MySQL, because it doesnt support functional indexes , so as soon as you do something like: ORDER BY ABS((start + stop)/2 - ?) it's no longer an indexed search It's a hard problem, even if you're using postgis . And even if you're a postGIS badass . Other than postGIS, there postgres...