Gaggle is a program that eases the passage of information between different programs i.e. geese. Cytoscape, one such goose, is used to organized and display networks so that it is easier to manage and draw conclusions from data. Genome Browser also organizes data. It displays a map of a genome and corresponding data to locations of interest. Firegoose retrieves information from databases such as KEGG and GO and converts the data into a format readable by Gaggle. The Translator converts gene information from one system to another. There are many other geese and the format of Gaggle allows programmers to modify programs to interact with Gaggle. Egrin, Environment and Gene Regulatory Influence Network, is a model, currently used for Halobacterium, made up of inferences produced by cMonkey and Inferelator. cMonkey is an algorithm that biclusters data, i.e. it looks at tables of information and searches for correlations in subsets of data. Inferelator is an algorithm that computes likely reactions, many about genes turning on or off, to certain stimuli via statistical analysis. MeDiChi is a program used to find transcription factor locations via data gained from the ChIP-chip method.

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