# Enhancements to the GMOD Suite of Genome Annotation and Visualization Tools

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA BERKELEY · 2024 · $663,262

## Abstract

Usability remains a significant barrier to broader adoption of cutting-edge bioinformatics
tools, due to a lack of user-friendly web interfaces. The Generic Model Organism
Database (GMOD) provides standards-based software components from which
web-facing genome databases can be quickly assembled. JBrowse, the genome
browser of GMOD, aims to "democratize" genome informatics by making genome
annotations and sequence analysis tools more accessible to the broader community of
biologists, using JavaScript and the dynamic web. JBrowse is now in active use by
thousands of websites and over a hundred thousand users, with over a million hits per
month. Its annotation editing plugin, Apollo, is used by many NIH-funded projects to
coordinate contributions from professional biocurators and motivated experts in the
community. In this phase of the JBrowse project, we plan to build machine learning
capabilities into JBrowse: to make automated recommendations to users that help them
more rapidly review evidence and form hypotheses, to help developers of AI tools
assemble and curate genomic datasets, and to present the results of machine learning
analyses of genomic data dynamically to the user on demand. We also propose to
enhance JBrowse's capabilities for using genomic synteny as a navigation tool to move
between related genomes, view evolutionarily conserved gene structures and their
associated alignments, and visualize genome annotations in their phylogenetic context.
We will also significantly improve JBrowse's speed and design via series of systematic
performance and usability benchmarks, and by user testing at design sprints. Finally,
we will continue GMOD's outreach/helpdesk efforts with focused workshops, training
materials, and documentation to maximize the utility of GMOD/JBrowse to the broader
community.

## Key facts

- **NIH application ID:** 10801225
- **Project number:** 2R01HG004483-15
- **Recipient organization:** UNIVERSITY OF CALIFORNIA BERKELEY
- **Principal Investigator:** Ian H Holmes
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $663,262
- **Award type:** 2
- **Project period:** 2024-03-01 → 2027-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10801225

## Citation

> US National Institutes of Health, RePORTER application 10801225, Enhancements to the GMOD Suite of Genome Annotation and Visualization Tools (2R01HG004483-15). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10801225. Licensed CC0.

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