Bioinformatics Infrastructure and Services

The Bioinformatics Infrastructure and Services Core provides support to all three CCMI projects at all stages of research and publication. The Core is made up of three major components: Cytoscape and the Cytoscape Cyberinfrastructure (CI); the Network Data Exchange (NDEx); and the CCMI Data and Analysis Portal. Cytoscape provides a range of tools for the analysis and visualization of biological networks. NDEx provides the database infrastructure to support the sharing, review and dissemination of network data and models. It also enables a consolidated access point to public biological network resources for use by CCMI investigators. Finally, the CCMI Data and Analysis Portal provides 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.

Outreach Core

The Outreach Core seeks to promote systems biology collaborations within UCSF, UCSD, Stanford University, and the larger cancer research community. The Core also seeks to educate clinicians how machine learning models can influence patient care. Significant effort is also devoted to educating the lay public about systems biology and its importance to society. Towards this effort, the core offers summer internships to high school and college students to train in cancer systems biology laboratories. We also host international and minority student internships in these laboratories to spark their interest in systems biology and its applications.