PATRIC Workshop Agenda – University of Florida

Published on 2015-07-10 00:00:00


Monday, July 13, 2015

8:30am            Register for PATRIC Account

9:00am            Overview of PATRIC

9:30am            Assemble a Genome in PATRIC

  • Uploading reads and read libraries

  • Selecting assembly methods for comparison

  • Queuing jobs and retrieving results

  • Analyzing assembly output and comparisons

  • Genome Assembly

10:30am          Break

10:45am          Annotate a Genome in PATRIC Using RASTtk

  • Uploading or selecting contigs in workspace

  • Selecting genome metadata and annotation options

  • Queuing jobs and retrieving results

  • Previewing an annotated genome

  • Genome Annotation

12:00pm          Lunch

1:00pm           Comparative Genomics: Protein Families and Pathways

  • Selecting sets of genomes for a study

  • Comparing by region, genes, proteins

  • Comparing pathways

  • Visualizing with heatmap viewer and downloads

  • Acinetobacter Use Case

5:00pm            Day 1: Adjourn

Tuesday, June 16, 2015

9:00am            Metabolic Modeling in PATRIC

9:45                 Proteomic Comparison

  • Selecting genomes for a study

  • Visualization of compared genomes

  • Download and analysis of results

  • Proteome Comparison

10:30am         Break

10:45am          RNA-Seq Pipeline, Downloading Data into PATRIC and differential expression

12:00pm          Lunch

1:00pm            Exploring Genes Identified by RNA-Seq and transcriptomic analysis

5:00pm            Day 2: Adjourn