PATRIC/RAST Workshop at Argonne National Laboratory, May 7-9, 2018

Published on 2018-01-22

The PATRIC/RAST teams will be offering a tutorial workshop May 7-9, 2018, at Argonne National Laboratory in the suburbs of Chicago, IL. The workshop will run for three days, with the third day optional and devoted solely to participants working on their own problems with help from the PATRIC/RAST team members.

The tutorial will show participants how to assemble a genome from reads, annotate that genome, and then compare that genome to the public genomes available in PATRIC using a suite of comparative analysis tools. In addition, participants will be able to annotate sequence variation, construct a metabolic model for their genome, load and analyze RNA-Seq data, and use the updated BLAST service. Participants will also learn to use PATRIC’s newest services including building phylogenetic trees, that include the ability to build a phylogenetic tree using PATRIC’s new tree-building pipeline, and do analysis of Tn-Seq data.

The workshop will be limited to 35 people on a first-come, first-served basis. While there is no fee for the workshop, participants are responsible for their own travel expenses. If you wish to participate, we encourage you to respond quickly at <>.

NOTE: All workshop attendees must also separately fill out the “Argonne Visitor Request” form at: <> as soon as possible — but especially non-U.S. Citizens, since they will take additional time to be cleared. Please enter Lisa Hundley, <>, for the “Sponsor’s e-mail address.”


Argonne National Laboratory

Building 240, Room 1404/1405

Argonne, IL 60439


Monday, May 7, 2018

 9:00 am   Register for PATRIC Account, Overview (

10:00 am   Assemble a Genome in PATRIC and Data Upload

11:00 am   Break

11:15 am   Annotate a Genome in PATRIC Using RASTtk

12:00 pm   Lunch

 1:00 pm   Proteomic Comparison

 2:00 pm   Break

 2:15 pm   Comparative Genomics: Protein Families and Pathways

 3:45 pm   Running PATRIC’s Tree Building Service

 4:30 pm   Question and Answer Session and Hands-on Work

 5:00 pm   Day 1 Adjourn

Tuesday, May 8, 2018

 9:00 am   BLAST at PATRIC

 9:45 am   Similar Genome Finder Service

10:00 am   Break

10:15 am   RNA-Seq Pipeline, Downloading Data into PATRIC and Differential Expression

11:15 am   Expression Data Import Service

12:00 pm   Lunch

 1:00 pm   Comparative Transcriptomics: Exploring Public and Private Expression Data

 2:00 pm   SNP and MNP Variation service

 3:00 pm   Metagenome Binning Service

 3:30 pm   Building a Metabolic Model

 4:30 pm   Question and Answer Session and Hands-on Work

 5:00 pm   Day 2 Adjourn

Wednesday, May 9, 2018

 9:00 am   Introduction to PATRIC Command Line Interface (CLI)

11:00 am   Break

11:15 am   Work with Your Private Data

12:00 pm   Lunch

 1:00 pm   Work with Your Private Data

 3:00 pm   Question and Answer Session and Hands-on Work

 4:00 pm   Workshop Concludes