Heterogeneity among cancers and differences within individual tumors continue to challenge the efforts to develop effective therapies. A multitude of data such as single cell sequencing, digital pathology, and medical imaging are being generated to captures heterogeneityacross multiple scales. However, data is siloed and connections between scales remains elusive. SimBioSys PhenoScope is a novel research tool to harmonize these disparate data elements, connecting the genomic, cellular/pathway, microscropic tissue environment, and tissue scales. The tool is being developed for use in biomarker discovery. Combining state-of-the-artmachine learning, dimensionality reduction techniques, novel spatio-temporal simulation algorithms, and support for public data repositories, PhenoScope provides a new means of assessing factors contributing to a cancer's phenotypical behavior, thereby allowing elucidation of new pharmacodynamic, prognostic, predictive,and surrogate biomarkers. During the Phase II contract, a beta version of the application will be developed. Specific activities will include: 1) support for clinical outcomes data, 2) capabilities for users to bring their own data, 3) an interactive scripting/data exploration environment, 4) compatibility and cloud deployment enhancements, and 5) beta testing with customers. This technology enables researchers to study cancer in a new light, and leads the way in to the upcoming phenomics era.