PATRIC May 2012 Release Introduces New Homepage, Workflow Pages, over 1200 New Genomes and More

Published on 2012-05-31

Website Enhancements

This release includes several completely redesigned areas of the PATRIC website, including a new homepage, several workflow pages, a consolidated tool landing page, and improved look and feel site-wide to enhance the PATRIC’s general usability.

Homepage

Working with representative users of the PATRIC community, our new homepage design philosophy promotes critical PATRIC tools, data pages and analysis capabilities.  The new homepage now includes:

  • A large amount of screen real-estate dedicated to showcasing explicit biologically-relevant workflows that illustrate how users can accomplish important tasks using PATRIC.  These workflows will be updated over time and are framed around interesting research questions in life-science.
  • Direct access to PATRIC’s BLAST interface.  This visually lightweight interface component allows users to copy-and-paste a nucleotide or amino acid sequence and BLAST against all PATRIC data with one click.  Access to advanced BLAST options is available from this interface as well.
  • A visual-mosaic of a subset of PATRIC’s most powerful tools.  Each tool is summarized in a few sentences and is accompanied by a thumbnail graphic.  At a glance, users can immediately see the breadth of tools PATRIC offers and can access a given tool of interest in just one click.
  • A revamped tag cloud depicting the most recently-accessed bacterial genomes at PATRIC as measured using live Google Analytics website traffic statistics.

Workflow Pages

PATRIC’s new workflow pages allow users to get a quick understanding of how to use a handful of  PATRIC pages and tools within the context of a biologically-relevant question.  We’ve purposely structured these workflow pages to appeal to biologists who may have similar research interests but are not aware of how best to leverage PATRIC to make their work easier.  We will be adding new workflow pages on a regular basis as we grow PATRIC’s suite of data and capabilities.  For this release we provide workflows describing how users may:

Each workflow includes detailed PATRIC screen images and instructive text in enough detail so that users can conduct similar workflows with data relevant to their datasets and/or interests.  Lastly, each workflow contains a number of links to other areas within PATRIC related to either tools and/or data pages illustrated in the workflow.

Tool Landing Page

With the number of PATRIC tools growing with each release, we now offer the PATRIC Tool Landing Page; a one-stop shop showcasing all of PATRIC’s tools categorized into four broad areas:  specialized searches, comparative analyses, annotation pipelines, and visual browsers.  In this release, the tool landing page offers quick summary and direct access to 17 tools. We have also updated PATRIC’s main navigation bar under “Searches & Tools” to reflect the full set of tools and categories.

Updated and Improved Look and Feel

We have updated PATRIC’s fonts, colors, and graphics to provide greater readability and visual scanning capabilities.  This allows us to present data-rich pages that are easy to read and understand. The new formatting also helps users find the information of interest within a given page with greater ease.  These improvements also include a streamlined PATRIC header with improved main navigation, as well as a redesigned footer where all social networking features are now grouped.

Genomes and Annotations

Since March 2012, 1273 new genomes have been added to PATRIC and 69 genomes have been updated. Total 1251 new genomes have been annotated using RAST.

A summary of the genomes available on the PATRIC website through May, 2012 is provided in the table below:

PATRIC

Legacy BRC

RefSeq

Number of genomes

5161

337

4829

Number of Complete genomes

1760

237

1770

Number of WGS genomes

3399

96

2659

Number of Plasmid only genomes

2

4

400