Workshop Description

The QCB Collaboratory is hosting a PATRIC Bioinformatics Resource Center Workshop, featuring Pipelines and Analysis Tools for Bacterial Genomes and ‘Omics Data. We encourage bacterial genomic researchers, students, and bioinformaticians to attend.  Workshop content includes:

• Genome assembly, annotation, Phylogenetic tree building
• RNA-Seq and Variation service pipelines: researchers can now assemble and annotate their raw reads, do SNP analysis and then analyze their genomes using the comparative analysis suite of tools
• Virtual integration of private data with all the public data available in PATRIC
• Virulence and antibiotic resistance data and information, along with other specialty gene information
• Free, downloadable data and analysis results
• Organism summaries; pre-sorted PubMed articles; interactive phylogenetic trees; and experimental data including transcriptomics, proteomics, protein structure, and protein-protein interactions
• Numerous interactive visualizations for genome browsing, multi-genome comparisons, pathway comparisons, protein family comparisons, phylogenetic trees with coupled MSAs, gene expression comparative analysis, genome metadata, transcriptomics data, 3-D protein structures, and more
• Personal workspace for creating/comparing groups of user-selected data and storing private data

Day 1

Pipelines and Analysis Tools for Bacterial Genomes and ‘Omics Data

8:00-8:30 Introduction, Registration
8:30-9:00 Assembly
9:00-9:30 Annotation
9:30-9:45 Similar Genome Finder
9:45-10:15 Tree Building
10:15-10:30 Break
10:30-11:00 Proteome Comparison tool
11:00-12:00 Comprehensive Genome Analysis
12:00-1:00 Lunch Break
1:00-1:45 RNA-Seq
1:45-2:15 Transcriptomic Analysis
2:15-2:30 Break
2:30-2:45 BLAST
2:45-3:15 Metagenomic Binning
3:15-3:45 Variation Analysis
3:45-4:15 Comprehensive Genome Analysis
4:15-5:00 Questions and wrap-up

Technical Requirements

The following system requirements are recommended for optimal PATRIC tool access and performance: Chrome, Safari, or Firefox browser (Internet Explorer is NOT recommended), Java Runtime Environment (JRE), and Adobe Flash Player.

Attendees are strongly encouraged to bring a laptop computer capable of accessing UCLA’s WiFi.


Rebecca Wattam, Ph.D.

Research Associate Professor, Biocomplexity Institute

Workshop Details

Prerequisites: None.
Length: 1 day, 8 hrs per day
Level: Intermediate
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 28

Fall 2018 Dates

August 29, 2018
8:00 AM – 5:00 PM