# The UCSC Genome Browser

> **NIH NIH U41** · UNIVERSITY OF CALIFORNIA SANTA CRUZ · 2020 · $1,376,687

## Abstract

This component describes our plans to enhance the interconnectivity of the UCSC Genome Browser and
related databases with other computational groups and tools in the scientific community, maintain the high
quality of the Genome Browser software and data, and provide a robust computing environment capable of
supporting our developers and users.
We propose three primary ways in which we plan to develop, use, and extend the data exchange standards
that make it easier for other bioinformaticians to both use our data and make their own data available in the
Genome Browser. We plan to further develop our widely adopted track and assembly hub systems that group
together genomics files in an organized fashion and label them for browser display, in particular by extending
the representation of metadata (such as biosample sources and treatments) in hubs, and expanding our
search capabilities. We will continue to work with ontology groups to incorporate their controlled vocabularies
into relevant fields of our metadata. We will closely collaborate with the Global Alliance for Genomics and
Health (GA4GH) project to ensure that their APIs are sufficiently flexible to express our data sets and to
develop a JSON-based web services API to our databases.
We plan to maintain and improve the quality of our software through the continued use of good engineering
practices, including the appropriate use of functional programming approaches to minimize code side effects
and maximize parallel processing potential. We will continue to employ incremental, object-oriented, modular
programming techniques and unit tests to maintain code quality, as well as our weekly paired-review process
that ensures a thorough review of new code and helps distribute knowledge of the code base throughout our
organization. Augmenting our engineering practices, we will continue to maintain a separate quality assurance
group that applies a combination of automated and manual testing to check the quality of the software and
data released on our website.
The Genome Browser production and development environments are supported by several mid-range server-
grade computers and a variety of storage subsystems chosen with good price/performance ratios in mind. We
plan to reconfigure our system to reduce single points of failure and increase parallelism, and will reduce our
need for a large compute cluster by making increased use of the cloud for large bursts of computation, such as
that associated with our multiple genome alignment pipeline.

## Key facts

- **NIH application ID:** 9969400
- **Project number:** 5U41HG002371-21
- **Recipient organization:** UNIVERSITY OF CALIFORNIA SANTA CRUZ
- **Principal Investigator:** William James Kent
- **Activity code:** U41 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $1,376,687
- **Award type:** 5
- **Project period:** 2001-07-12 → 2022-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9969400

## Citation

> US National Institutes of Health, RePORTER application 9969400, The UCSC Genome Browser (5U41HG002371-21). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9969400. Licensed CC0.

---

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