# CORE 1: Data Management and Bioinformatics

> **NIH NIH U19** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2021 · $597,170

## Abstract

CORE 1: DATA MANAGEMENT AND BIOINFORMATICS CORE
SUMMARY
The ​Data Management and Bioinformatics Core will support the two HPMI projects at all stages of research
and publication. The core will be composed of three major components: Cytoscape and the Cytoscape
Cyberinfrastructure (CI); the Network Data Exchange (NDEx); and the HPMI Data and Analysis Portal. First,
Cytoscape will provide a range of tools for the analysis and visualization of biological networks, including the
protein-protein interaction networks from ​Project 1​, the genetic interaction networks from ​Project 2​, as well as
the hierarchical cell ontologies and models from both projects. The second component, NDEx, will provide
database infrastructure to support the sharing, review and dissemination of network data and models. It will
also enable consolidated access to public biological network resources for use by HPMI investigators. Finally,
the HPMI Data and Analysis Portal will provide a common access point for software tools and pipelines and for
their associated data. This component will be supported by GenePattern Notebooks, which will facilitate the
development of workflow pipelines and the sharing and reproducibility of analyses. The above three
components – visual network maps in Cytoscape, storage of networks and models in NDEx, and software and
analysis workflows in GenePattern​ Notebooks – will all be made accessible through the HPMI’s website.
Publications using HPMI products will be enhanced by the recent additions to Cytoscape for dynamically
embedding network data in peer-reviewed journals. Finally, the Core will draw on an impressive array of
hardware infrastructure for supercomputing, including high performance clusters at multiple sites.

## Key facts

- **NIH application ID:** 10224014
- **Project number:** 5U19AI135990-04
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** Trey Ideker
- **Activity code:** U19 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $597,170
- **Award type:** 5
- **Project period:** 2018-08-17 → 2023-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10224014

## Citation

> US National Institutes of Health, RePORTER application 10224014, CORE 1: Data Management and Bioinformatics (5U19AI135990-04). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10224014. Licensed CC0.

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