MED-Fly Outbreak and Eradication Simulation
MED-FOES is an implementation of a stochastic Agent-Based Simulation (ABS) system for analysing demographic changes in a single population of Medfly (Ceratitis capitata) over time. The simulation currently takes population extinction as a given because it aims to give us better estimates of necessary quarantine lengths in areas where Medfly is not currently established but does repeatedly invade. Thus the objective of this software is to estimate the time to local extirpation based on known ranges of developmental, survivorship and reproductive parameters, as well as assumed ranges of an eradication pressure parameter.
RNAseq expression analysis.
RNAseqR is designed for expression analysis of RNA-seq data, and is best suited for analysis of multiple, unreplicated libraries. It is a C++ coded program currently compiled for Linux systems.
With GUI and command line interfaces, it can do log, PPM, and/or RPKM (if lengths provided) transformations, as well as, statistical analysis for differential expression, using the negative binomial cumulative distribution function (CDF) or the R test statistic introduced for EST analysis by Stekel, et al.
Output allows for decisions based on CDF probabilities, top R values, or comparison of R values with randomized data. Comparisons are the believability metric of Stekel et al, or observed vs expected R at a given mean expression. Randomization is through Poisson or negative binomial distributions, or column shuffling.
Download at sourceforge.net (opens in new window)