Evaluating Genome Browsers Using a Software Qualification Method Evaluation

Abstract

National audienceBackground: Because Genome Browsers (GBs) hold a central place in genomic projects, the diversity of tools available to scientists for visualizing and exploring genomes has increased dramatically over the last years. It often turns out to be a daunting task to compare and choose a well-adapted GB, as multidisciplinary knowledge is required to carry out this task and the number of tools, functionalities and features are overwhelming. To help the interested community making informed choices, there is an urgent need to apply and adapt standard software evaluation processes to bioinformatics tool families, such as GBs. Results: We have implemented an industry promoted software qualification method, QSOS, to evaluate many of the available GBs using more than 120 criteria. We have defined about half of those criteria specifically for GBs, and incorporated the other half directly from QSOS’s generic section. We have evaluated six GBs according to this methodology and present here a subset of our results organized according to three different user profiles: a biologist whose interest primarily lies into user-friendly and informative functionalities, a bioinformatician who wants facilities to integrate the GB into a wider framework, and a computer scientist who might choose a GB according to more technical features, for instance the possibility of developing a customized version by modifying the source code. Conclusions: A website is publicly available at the URL http://genome.jouy.inra.fr/CompaGB. It offers a dedicated framework for GBs evaluation and comparison. It has been set up to help scientists to (1) choose GBs that would better fit their particular project, (2) visualize GBs features comparatively with easily accessible formats, such as tables or radar plots and (3) perform their own evaluation against the defined criteria