CORE 1: DATA MANAGEMENT AND BIOINFORMATICS CORE SUMMARY The ?Data Management and Bioinformatics Core will support the two HPMI projects at all stages of research and publication. The core will be composed of three major components: Cytoscape and the Cytoscape Cyberinfrastructure (CI); the Network Data Exchange (NDEx); and the HPMI Data and Analysis Portal. First, Cytoscape will provide a range of tools for the analysis and visualization of biological networks, including the protein-protein interaction networks from ?Project 1?, the genetic interaction networks from ?Project 2?, as well as the hierarchical cell ontologies and models from both projects. The second component, NDEx, will provide database infrastructure to support the sharing, review and dissemination of network data and models. It will also enable consolidated access to public biological network resources for use by HPMI investigators. Finally, the HPMI Data and Analysis Portal will provide a common access point for software tools and pipelines and for their associated data. This component will be supported by GenePattern Notebooks, which will facilitate the development of workflow pipelines and the sharing and reproducibility of analyses. The above three components ? visual network maps in Cytoscape, storage of networks and models in NDEx, and software and analysis workflows in GenePattern? Notebooks ? will all be made accessible through the HPMI?s website. Publications using HPMI products will be enhanced by the recent additions to Cytoscape for dynamically embedding network data in peer-reviewed journals. Finally, the Core will draw on an impressive array of hardware infrastructure for supercomputing, including high performance clusters at multiple sites.
| Batra, Jyoti; Hultquist, Judd F; Liu, Dandan et al. (2018) Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication. Cell 175:1917-1930.e13 |
| Shah, Priya S; Link, Nichole; Jang, Gwendolyn M et al. (2018) Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis. Cell 175:1931-1945.e18 |
