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Harry is a small tool for comparing strings and measuring their similarity. The tool supports several common distance and kernel functions for strings as well as some excotic similarity measures. The focus of Harry lies on implicit similarity measures, that is, comparison functions that do not give rise to an explicit vector space. Examples of such similarity measures are the Levenshtein distance and the Jaro-Winkler distance. For comparison Harry loads a set of strings from input, computes the specified similarity measure and writes a matrix of similarity values to output. The similarity measure can be computed based on the granularity of characters as well as words contained in the strings. The configuration of this process, such as the input format, the similarity measure and the output format, are specified in a configuration file and can be additionally refined using command-line options. Harry is implemented using OpenMP, such that the computation time for a set of strings scales linear with the number of available CPU cores. Moreover, efficient implementations of several similarity measures, effective caching of similarity values and low-overhead locking further speedup the computation. Harry complements the tool Sally that embeds strings in a vector space and allows computing vectorial similarity measures, such as the cosine distance.

The microPIECE (microRNA pipeline enhanced by CLIP experiments) takes the AGO-CLIP data from a speciesA and transfers it to a speciesB. Given a set of miRNAs from speciesB it then predicts their targets on the transfered CLIP regions. Github repository: https://github.com/microPIECE-team/microPIECE

Minor update on release 2015.1

First release of the ModelFactory Toolbox