Core 2: Software Infrastructure for Network Models and Cell Maps

CCMI v2.0 Core 2: Software Infrastructure for Network Models and Cell Maps Core Lead: Trey Ideker; Co-Investigator: Dexter Pratt SUMMARY The Software Infrastructure for Network Models and Cell Maps Core will support the CCMI Projects at all stages of research and publication. The core will provide infrastructure and assistance towards three main elements: (1) the Cytoscape desktop application along with tools and services from the Cytoscape Ecosystem; (2) NDEx, the Network Data Exchange; and (3) infrastructure for the development and deployment of web services and applications. First, we will support center investigators in use of the Cytoscape Ecosystem for analysis and visualization of biological networks, including protein--protein interaction networks from Project 1, genetic interaction networks from Project 2, and multiscale cancer cell maps from Project 3. The Cytoscape Ecosystem includes the well-known Cytoscape desktop environment, the HiView multiscale cell model viewer, the IQuery pathway analysis tool, multiple R and Python libraries, and the CDAPS software framework for the generation of multiscale cell models. Second, we will facilitate the use of NDEx by center investigators to publish CCMI cell maps, interaction data, and other products as “live” network data that can be immediately visualized and used. We will also provide assistance in the use of NDEx to share pre-publication network data between center investigators, including direct, programmatic access from Jupyter notebooks and other software. Third, we will provide assistance to Project 3 investigators in the creation of web interfaces and back-end services. For all projects, we will facilitate programmatic access to resources, hosting of websites, the use of Docker software containers, and the management of CCMI Github repositories. Finally, we will maintain and extend the CCMI web portal to provide access to (1) CCMI public networks and cell maps via the NDEx networks cloud, (2) CCMI software tools and resources, (3) custom websites and web applications CCMI v2.0