Usage Overview

Users and client systems interact with the GLUE database and its bioinformatics functionality via the Command Layer.

Further GLUE command functionality is available via Modules, which provide built-in functionality customizable for each project.

Users may also create project-specific functionality via the Scripting Layer.

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Core GLUE Commands

The core set of GLUE commands supports operations such as:

• Adding, deleting, or modifying objects in the database
• Querying the database using a flexible query language
• Calculating frequencies of amino acid residues within specific sequences
• Scanning sequences for specific nucleotide or amino acid patterns

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Module-Based Functionality

GLUE’s extensive module-based functionality includes:

• Importing sequences into the database from NCBI Nucleotide
• Extracting and normalizing data from GenBank records
• Computing new alignments
• Assigning genotypes to sequences using a maximum-likelihood-based method
• Exporting sequences or alignments from the database for external use

Modules also provide interfaces to bioinformatics tools such as BLAST, RAxML, and MAFFT, allowing users to integrate these tools into their GLUE workflows.

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Scripting Layer

The GLUE scripting layer adds another way to use GLUE functionality. It allows you to add custom logic to your GLUE projects in the form of JavaScript programs. These programs run within the GLUE engine. They may run GLUE commands in the context of other computations. They can also be encapsulated within modules, allowing your custom logic to be invoked from other parts of the project. The main uses of the scripting layer are:

• To execute a step in your project build. Using the scripting layer here means the build can use more complex, dynamic logic.
• To perform some analysis of project data. The scripting layer may access any part of the GLUE project, using any GLUE command, so it can be used to execute code associated with a research question.

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