Computational biology is the combined application of math, statistics and computer science to solve biology-based problems. Examples of biology problems are: genetics, evolution,cell biology, biochemistry. JOURNAL OF COMPUTATIONAL BIOLOGY provides a forum for communicating scientific and technical issues associated with the analysis and management of biological information at the molecular level. It will accept papers on the computational, mathematical, and statistical aspects of molecular biology. This includes sequence, comparison; sequence analysis and searching; DNA and protein sequence determination DNA topological structure; protein structure; RNA secondary and tertiary structure; genetic mapping; physical mapping; molecular evolution, including phylogenetic reconstructions; parallel methods of computation design and implementation of biological databases biological expert system design and use application of artificial intelligence methods to biological systems. It is becoming clear that quantitative models are needed to unravel the complexities of many biological systems. In this manuscript Bernasek et al. introduce a computational framework that automates the quantification of mosaic analysis for Drosophila imaginal discs, a common setting for studies of developmental processes. They validate the performance of their framework using both real and synthetic data.