PATRIC Workshop Agenda – University of Florida

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

AGENDA

Monday, July 13, 2015

8:30am            Register for PATRIC Account

9:00am            Overview of PATRIC www.patricbrc.org

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

• Metabolic Model Reconstruction

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

• Uploading RNA-seq data

• Selecting genomes and mapping

• Downloading and using data in PATRIC

• RNA Seq Analysis

• Differential expression

• Differential Expression

12:00pm          Lunch

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

• Exploring gene expression in datasets available in PATRIC

• Gene Expression

• Downstream analysis of RNA-Seq genes

• Examining the genes identified as significantly expressed by RNA

• Looking for data on antibiotic resistance genes

• Pseudomonas AR genes

5:00pm            Day 2: Adjourn