Bubble Sets is a visualization technique for dynamically creating ‘bubble’ borders around sets of visual objects, while avoiding inclusion of items not in the set. The project was previously implemented as an extension to the prefuse Java visualization toolkit. I have released a stand alone (no prefuse required) open source Bubble Sets library on github (thanks Josua Krause for creating a testing application)! The Bubble Sets technique and software were used in two best paper winners at the BioVis 2011 Symposium, HiTSEE: A Visualization Tool for Hit Selection and Analysis in High-Throughput Screening Experiments by Enrico Bertini et al., and RuleBender: Integrated Visualization for Biochemical Rule-Based Modeling by Adam M. Smith et al.
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