# Core 2: Software Infrastructure for Network Models and Cell Maps

> **NIH NIH U54** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2023 · $77,419

## Abstract

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

## Key facts

- **NIH application ID:** 10704622
- **Project number:** 5U54CA274502-02
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** Trey Ideker
- **Activity code:** U54 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $77,419
- **Award type:** 5
- **Project period:** 2022-09-14 → 2027-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10704622

## Citation

> US National Institutes of Health, RePORTER application 10704622, Core 2: Software Infrastructure for Network Models and Cell Maps (5U54CA274502-02). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10704622. Licensed CC0.

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