# CYTOSCAPE: AN ECOSYSTEM FOR NETWORK GENOMICS

> **NIH NIH U24** · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2023 · $1,441,919

## Abstract

CYTOSCAPE: AN ECOSYSTEM FOR NETWORK GENOMICS
PROJECT SUMMARY
Cytoscape is an open source software platform for biological network analysis, visualization and modeling. It is
a critical bioinformatics resource in academia and industry, with 300,000+ downloads per year and 25,000+
citations. The widespread adoption of Cytoscape is due mainly to its utility in diverse biological analyses, its
sustainable open development model, and its extensible architecture, which enables anyone to add algorithmic
functionality and has attracted hundreds of third-party developers.
Access to network analysis tools is particularly important now, at a time when network knowledge and
concepts are increasingly central to genomics research. Cytoscape is in an excellent position to address this
need and serve as a hub for knowledge-based genome analysis. In this application to support Cytoscape as a
U24 Genomic Community Resource, we will work towards four specific aims. First, we will maintain our
longtime substantial commitment to produce Cytoscape software as a critical research resource. Second, we
will complete our ongoing development of Cytoscape as an ecosystem of tools and services on the web, so
that key network biology tools are more accessible to biomedical researchers and can readily access big
biomedical datasets and interoperate in cloud computing environments. Immediate targets of these
developments will be resources in which federal organizations are already making substantial investments,
including AnVIL, BioData Catalyst and Cancer Genomic Data Commons. Third, we will work collaboratively
with outside tool developers to promote a constellation of leading tools for network-based genomic analysis,
including both existing and nascent approaches emerging from the data science community. Finally, we will
continue to offer a rich set of Cytoscape training programs, including new material that actively guides users
through analysis workflows, updating content based on input they provide.
In summary, these activities will support not only production of the Cytoscape resource– they will create a next
generation desktop, web and cloud-based ecosystem for using knowledge networks in genomic data science.

## Key facts

- **NIH application ID:** 10694852
- **Project number:** 5U24HG012107-02
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN DIEGO
- **Principal Investigator:** Trey Ideker
- **Activity code:** U24 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $1,441,919
- **Award type:** 5
- **Project period:** 2022-09-01 → 2027-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10694852

## Citation

> US National Institutes of Health, RePORTER application 10694852, CYTOSCAPE: AN ECOSYSTEM FOR NETWORK GENOMICS (5U24HG012107-02). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10694852. Licensed CC0.

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