User Guides

The PATRIC website provides an entry point to integrated data and tools for bacterial infectious disease research. The website is organized by data types and analysis tools. These User Guides serve as a reference for each of the tools and services including information on what it does, where it is located, and each of the features.

Contents:

• Organisms
• Data
• Workspace, Private Data, Groups, Jobs
• Services and Tools
• Global Search
• Registration
• Website Views, Tables, Filters, Action Bar
• System Requirements
• Data Submission in PATRIC
• FTP Site

Primary access to these tools is provided through the PATRIC main menu which is available at the top of the home page. The main menu provides the following options:

• Organisms - links to bacterial data sorted into genera. On each organism page, further divisions of data types are available from the data tabs such as Overview, Taxonomy, Phylogeny, Genome List, Feature Table, Specialty Genes, etc.

• Data - links to specialized “Data Landing Pages” that provide overview and summary information of PATRIC data, including pages for Antibiotic Resistance, Genomes, Genome Features, Pathways, Protein Families, Specialty Genes, Transcriptomics, and special featured data sets.

• Workspaces - links to the private workspace and subdirectories in the private workspace.

• Services - links to data processing and analysis pipelines in PATRIC. Currently, services are available for processing user-supplied data including Genome Assembly, Genome Annotation, BLAST, Variation Analysis, Expression Data Integration, RNA-Seq Analysis, Protein Family Sorter, Proteome Comparison, Pathway Comparison, and Model Reconstruction.

• Help - links to documentaion pages containing a PATRIC Quickstart video, User Guides, Tutorials, Webinars, and information to Provide Feedback.

• Global Search - searches PATRIC databases to quickly locate genomes, genes, and other information via keywords.

• Registration - allows creation of a PATRIC account, enabling use of PATRIC services and a private workspace. Other information (the three-line “hamburger” icon on the top right of the page) - links to pages containing additional information such as News, Publications, About PATRIC, Citing PATRIC, Scientific Working Group, Personnel, Collaborators, Related Sites, and System Architecture.

• 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 PATRIC’s features and functionality successfully.

A “PATRIC Quickstart” video tutorial providing an overview of the PATRIC website is also available from the Help Menu .