Quick Reference Guides

The MAAGE website resource provides an entry point to integrated data and tools for viral and bacterial infectious disease research. The website is organized by data types and analysis tools. These Quick Reference Guides provide summary information for each of the components of the website, including information on what the component is, what it does, where it is located, and an overview of its features.

Contents:

• Organisms and Data Types
• Advanced Searches
• Tools & Services
• Workspaces and Groups
• Global Search
• Registration and Sign In
• Website Views, Tables, Filters, Action Bar
• System Requirements
• FTP Site

Primary access to these components is provided through the MAAGE main menu which is available at the top of the home page. The main menu includes the following options:

• Organisms - links to bacterial and viral data sorted into genera and families, respectively. On each organism page, further divisions into data types are available from the data tabs such as Overview, Taxonomy, Phylogeny, Genome/Strain List, Gene/Features, Protein Families, Protein Structures, etc.

• Searches - links to specialized advanced searches across the various data types in MAAGE.

• Services and Tools - links to data processing and analysis pipelines in MAAGE. Currently, services are available for processing user-supplied data including Genome Assembly, Genome Annotation, BLAST, Variation Analysis, RNA-Seq Analysis, Protein Family Comparison, Proteome Comparison, Pathway Comparison, and others.

• Workspace, Private Data, Groups, Jobs - links to the private workspace and subdirectories in the private workspace; service jobs; and private genomes.

• Help - links to documentaion pages containing Quick Reference Guides, Tutorials, Webinars, and information to Provide Feedback.

• About - links to pages containing additional information such as About MAAGE, Contact Us, Our Team, Announcements, Outreach, Publications, Citations, Related Resources, and the MAAGE GitHub code repository.

• Registration / Sign In - allows creation of a MAAGE account, enabling use of MAAGE services and a private workspace. Alternatively, users can use the “Sign In” option if they already have a MAAGE account. After logging in, these options are replaced with a person icon, which provides access to the user’s account settings and the option to log out.

• Views, Tables, Action Bar - Common navigation elements and tools throughout the website.

• System Requirements - Minimal hardware and software needs for the user’s computer in order to be able to use MAAGE’s features and functionality successfully.