= Core 4: Integrated Visualization and Analysis of Biological Context =
== Specific Aims ==
 * Specific Aim 1: Develop and deploy extensions to Cytoscape and Chimera that will support the integration of macromolecular structural visualization and analysis with network visualization and analysis.
  * Aim 1A: Enhance and extend structureViz to support a broader range of use cases, including more complicated relationships between network objects (nodes and edges), their attributes, and structures or parts of structures displayed in Chimera.
  * Aim 1B: Develop and deploy a plugin and any required Cytoscape core modifications to support the Chimera extension described in Core 1 to "zoom out" from the structural context to the broader network context.
 * Specific Aim 2: Develop and deploy tools to support the analysis of high-throughput data (genetic, mRNA expression, RNA-Seq, ChIP-Seq, Hi-C) in the context of biological pathways, protein-protein interaction networks, or other biological network representation.
  * Aim 2A: Extend existing clustering tools to support fuzzy clustering
  * Aim 2B: Support visualizations and analyses that allow comparisons between species, conditions, and time series data
  * Aim 2C: Investigate the potential value of a 3D visualization of Hi-C epigenetic data
 * Specific Aim 3: Support the investigation of protein function through the visualization and analysis of protein similarity networks.
  * Aim 3A: Extend and enhance Cytoscape plugin to improve usability and functionality.  Specifically, add support to allow end-users to visualize their proteins in the context of SFLD similarity networks.
  * Aim 3B: Support the interactive visualization of very large networks.
 * Specific Aim 4: Improve the overall Cytoscape user experience for RBVI collaborators and DBPs
  * Aim 4B: Improve grouping by visually identifying grouped nodes and allowing for progressive disclosure concepts with the Cytoscape core.
  * Aim 4C: Add new techniques for visually mapping data to network elements such as nodes and edges.