# Cytoscape: A Modeling Platform for Biomolecular Networks

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2020 · $687,759

## Abstract

CYTOSCAPE: A MODELING PLATFORM FOR BIOMOLECULAR NETWORKS
SUMMARY
Cytoscape is an open source bioinformatics environment for biological network analysis, visualization and
modeling. It has grown to become a standard resource in academia and industry, due mainly to its timeliness
(it was one of the first tools for visualization of biological networks), open development model (it is still one of
few such tools that is open-source) and public App interface (allowing anyone to add functionality to Cytoscape
and attracting hundreds of third-party developers and industrial partners). Cytoscape usage continues to
increase significantly, doubling over the past three years to ~208,000 downloads in 2016. The NIH has funded
Cytoscape development since 2004 under the “Continued Development and Maintenance of Software” group
of programs (R01 GM070743).
In this competitive renewal, we will improve, maintain, and support Cytoscape along four Specific Aims. First,
we will substantially increase the resources available in Cytoscape for the study of human genetic variants in
individual human genomes and across cohorts of individuals. We will ensure access to key molecular networks
for humans and human disease, implement direct import of human sequence variants and add a network
propagation engine for identifying genetic variants impacting the same network neighborhoods and pathways.
Second, we will develop Cytoscape into a useful clinical recommendation system, where researchers, and
ultimately clinicians, can score a patient as being part of a particular class (​e.g., case or control, disease
subtype) based on the surrounding patient similarity network. This will be based on our recently developed
netDx computational method that classifies patients into subtypes based on diverse clinical and genomic data.
Third, we will develop a system of Cytoscape workflows based on Jupyter Notebooks and web services,
allowing flexible automation, access to new data types, and more fluid interchange of network analyses.
Fourth, we will maintain and disseminate Cytoscape using a modern software management process, and we
will continue to work with scientific journals to integrate Cytoscape-based network and workflow viewers into
scientific publications.
Cytoscape is an important milepost on the road to developing large-scale “circuit diagrams” of human biology
and disease. Continued support of Cytoscape will allow other laboratories to avoid reinventing the same tools,
time that can instead be devoted to more complex analyses or to basic research.

## Key facts

- **NIH application ID:** 9966008
- **Project number:** 5R01HG009979-17
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN DIEGO
- **Principal Investigator:** Trey Ideker
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $687,759
- **Award type:** 5
- **Project period:** 2004-06-01 → 2022-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9966008

## Citation

> US National Institutes of Health, RePORTER application 9966008, Cytoscape: A Modeling Platform for Biomolecular Networks (5R01HG009979-17). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/9966008. Licensed CC0.

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