Gifford Lab GLUE Projects

Background

The vision for GLUE emphasized synergy between different areas of genomics-related virus research, enabling collaborative use of both data and analytical methods across different usage contexts. The projects listed in this section showcase how GLUE can serve as a foundation for development of wide-ranging kinds of genomics resources.

While the majority of GLUE projects in this collection focus on viral genomics, some have been developed for transposons and gene families, illustrating the versatility of GLUE beyond viruses. The virus projects address many of the unusual features of viral genomes, such as circular genomes, segmented genomes, and frameshifting translation mechanisms.

How can the GLUE Projects be Used?

Direct Research Use: GLUE projects offer curated databases featuring pre-collected, annotated sequences, metadata, and ready-made alignments. These resources enable researchers to perform complex bioinformatics analyses without needing to assemble datasets from scratch.
Advanced Tools for Analysis and Integration: GLUE includes powerful inbuilt tools for analyzing and manipulating curated genomic data, alignments, and phylogenetic trees. It also features modules for seamless integration with external tools, such as BLAST, MAFFT, and RAxML, enhancing its versatility and enabling complex bioinformatics workflows directly within the framework.
Customizable Data Processing Pipelines: GLUE's command and scripting layer can be used to implement sequence data-processing pipelines. Some GLUE projects include pre-built pipelines for processing sequence data. Among these, applications in genomic epidemiology—such as virus surveillance, variant tracking, and monitoring antiviral drug resistance—demonstrate how GLUE projects support public and animal health initiatives.
Web Resources: Some GLUE projects provide a web user interface (UI), enabling their deployment as online databases accessible via a browser. For projects without a built-in UI, developers can use existing templates or create custom interfaces to make the data easily accessible online.
Integration into Organizational Infrastructures: GLUE can be deployed within a standard web server, exposing its functionality via standard web service protocols. This enables seamless machine-to-machine interaction, supporting the development of interactive public websites, programmatic services, or integration into an organization’s computing infrastructure as part of a microservices software architecture. This capability broadens the scope of how GLUE projects can be utilized and scaled in modern computational environments.
Templates for New Resources: For those interested in using GLUE to develop new resources for viruses, transposons, or gene families, the GLUE projects distributed here - which contain many re-usable components - can serve as flexible templates.
Data Reusability Outside of GLUE: Adhering to a data-oriented programming philosophy, GLUE projects preserve original data in a way that allows researchers and developers to repurpose the organized data outside of GLUE, providing flexibility for use in other platforms and tools without dependency on the GLUE software framework.

Projects by Category

Projects have been grouped into categories below. Some projects occur in more than one category, and are listed in each.

Warning

Some GLUE projects with web user interfaces are hosted as online databases and analysis tools by third-party institutions (e.g., universities). While links to these instances are provided, they are hosted and maintained independently of the Gifford Lab, and we cannot ensure their ongoing availability or maintenance.