Here we describe a selection of pieces of software written by BioSS staff.
MicroPop: R package for modelling microbial Populations and Communities
Microbial communities perform highly dynamic and complex ecosystem functions that impact plants, animals and humans. MicroPop is a piece of software which attempts to model the dynamics of microbial interactions for a wide range of microbial systems. It is the result of an interdisciplinary project resulting from a collaboration between Helen Kettle and The Rowett Institute (Petra Louis and Harry Flint).
Number Muncher Diets
Number Muncher Diets is a computer program developed by Biomathematics and Statistics Scotland (BioSS) and the Rowett Institute from their research funded principally by the Scottish Government. The program uses mathematical methodology to create a "weekly shopping list", offering a selection of food items that satisfies a combination of criteria based on data input in the form of published nutritional guidelines, costs, environmental impact, and personal food preferences.
Try it out!
StagePop - modelling stage-structured populations in R
StagePop enables ecologists to model the dynamics of populations that are stage-structured (those in which individuals transition between distinct stages, e.g. eggs, juveniles, adults for most insects). Although initially developed to model the impact climate change may have on populations whose development rates are temperature dependent, such as potato cyst nematodes, its capability is much more general, including modelling interacting species in complex food webs.
DUST - Over-Years Uniformity
The DUST environment for evaluating data from Distinctness, Uniformity and STability crop trial results is being enhanced with an improved method for analysing plant uniformity. This new methodology will be implemented in the UK, and then internationally. There is also an R package.
TetraploidSNPMap is a programme for constructing linkage maps and carrying out QTL mapping for populations of auto -tetraploid species (e.g. those with chromosomes in sets of four rather than in pairs), especially potato. The original TetraploidMap for Windows was published in 2007, but it has now been revised to handle the advances in size and information content of new genetic marker technologies, such as single nucleotide polymorphism (SNP) data from the Infinium 8300 potato SNP array.