# Administrative Supplement for Equipment in Support of NRNB Aims

> **NIH NIH P41** · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2023 · $149,176

## Abstract

OVERALL - PROJECT SUMMARY
The mission of the National Resource for Network Biology (nrnb.org) is to advance the science of biological
networks by creating leading-edge bioinformatic methods, software tools and infrastructure, and by engaging
the scientific community in a portfolio of collaboration and training opportunities. Much of biomedical research is
dependent on knowledge of biological networks of multiple types and scales, including molecular interactions
among genes, proteins, metabolites and drugs; cell communication systems; sample similarity networks;
relationships among genotypes and biological and clinical phenotypes; and patient and social networks. NRNB
technologies, like Cytoscape, are among the most widely used software tools in biology, with tens of thousands
of active users, and enable researchers to analyze these networks and use them to better understand biological
systems and how they are reprogrammed in disease. Since 2010, the NRNB has been supported as a
Biomedical Technology Research Resource of the National Institute of General Medical Sciences.
 NRNB’s three technology research and development efforts seek to introduce innovative concepts with the
potential to transform network biology, transitioning it from a static to a dynamic science (TR&D Project 1); from
flat network diagrams to multi-scale hierarchies of biological structure and function (Project 2); and from
descriptive interaction maps to interpretable and predictive network models (Project 3). In previous funding
periods our technology projects have produced novel and highly cited approaches, including network-based
biomarkers for stratification of disease, data-driven gene ontologies assembled completely from network data,
and deep learning models of cell structure and function built using biological networks as a scaffold. NRNB has
also produced widely adopted software infrastructure, including the Cytoscape ecosystem; the cBioPortal for
cancer genomes and pathways; the GeneMANIA network query and gene function prediction tool; the NDEx
biological networks cloud; and WikiPathways for biological pathway curation.
 During the next period of support, we introduce dynamic regulatory networks formulated from single-cell
transcriptomics data (TR&D1); efficient algorithms for detection of hierarchical structure and pleiotropy in
biological networks (TR&D2); and procedures for using networks to seed machine learning models of drug
response that are both mechanistically interpretable and transferable across biomedical contexts (TR&D3).
These efforts are developed and applied in close collaboration with outside investigators from 19 Driving
Biomedical Projects (DBPs) who specialize in experimental generation of network data, disease biology (cancer,
neuropsychiatric disorders, diabetes), single-cell developmental biology, and clinical trials. TR&Ds are also
bolstered by 7 Technology Partnerships (TPs), in which NRNB scientists coordinate technology development
with l...

## Key facts

- **NIH application ID:** 10799346
- **Project number:** 3P41GM103504-14S1
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN DIEGO
- **Principal Investigator:** Trey Ideker
- **Activity code:** P41 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $149,176
- **Award type:** 3
- **Project period:** 2010-09-13 → 2025-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10799346

## Citation

> US National Institutes of Health, RePORTER application 10799346, Administrative Supplement for Equipment in Support of NRNB Aims (3P41GM103504-14S1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10799346. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*