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

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA BERKELEY · 2020 · $680,475

## 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 tens of thousands of users. In this phase of the project, we
plan to build a synteny browser into JBrowse, so that users can rapidly navigate
between related genomes, view evolutionarily conserved gene structures and their
associated alignments, and visualize genome annotations in their phylogenetic context.
This synteny browser will have the same responsiveness and interactivity as JBrowse,
with smooth panning, zooming, filtering, sorting, and searching available as
drag-and-drop operations from within the web browser. We will also significantly
improve JBrowse's performance at scale: many JBrowse instances have hundreds or
thousands of tracks, demanding efficiency optimizations, more compact visualization,
and user interface enhancements to promote data "discoverability". We will develop a
graphical interface for customizing JBrowse, configuring its appearance and behavior,
and installing plugins, in the style of the Wordpress blog platform. We will build on the
newly-developed JBrowse analysis server to make standard read-to-reference
alignment tools (BWA and BowTie) available to users from within the browser, and we
will make new visualizations available for RNA-Seq, population genomics, epigenomics,
and other data types. 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:** 9920732
- **Project number:** 5R01HG004483-12
- **Recipient organization:** UNIVERSITY OF CALIFORNIA BERKELEY
- **Principal Investigator:** Ian H Holmes
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $680,475
- **Award type:** 5
- **Project period:** 2007-09-01 → 2023-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9920732

## Citation

> US National Institutes of Health, RePORTER application 9920732, Enhancements to the GMOD Suite of Genome Annotation and Visualization Tools (5R01HG004483-12). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9920732. Licensed CC0.

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