PATRIC/RAST Workshop at Argonne National Laboratory, November 14-16, 2017

Published on 2017-09-08

The PATRIC/RAST teams will be offering a tutorial workshop on 2017-November 14-16, 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 be walked through PATRIC’s newest services 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 <rast-workshop@mcs.anl.gov>.

NOTE: All workshop attendees must also separately fill out the “Argonne Visitor Request” form at: <https://apps.anl.gov/registration/visitors> as soon as possible — but especially non-U.S. Citizens, since they will take additional time to be cleared. Please enter Karen VanMeerten, <vanmeert@anl.gov>, for the “Sponsor’s e-mail address.”

LOCATION

Argonne National Laboratory

Building 240, Room 1406/1407

Argonne, IL 60439

DRAFT AGENDA

Tuesday, November 14, 2017

9:00 am           Register for PATRIC Account, Overview (www.patricbrc.org)

10:00 am         Assemble a Genome in PATRIC and Data Upload
Uploading reads and read libraries
Selecting assembly methods for comparison
Queuing jobs and retrieving results
Analyzing assembly output and comparisons

11:00 am         Break

11:15 am         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

12:00 pm         Lunch

1:00pm            Proteomic Comparison
Selecting genomes for a study
Visualizing compared genomes
Downloading and analyzing the results

2:00 pm           Break

2:15 pm           Comparative Genomics: Protein Families and Pathways
Creating a genome group
Comparing by region, genes, proteins
Comparing pathways
Visualizing with heatmap viewer and downloads
Finding specific differences, downloading and saving results into private workspace

3:45 pm           Running PATRIC’s Tree Building Service
Creating ingroup genomes
Creating outgroup genomes
Submitting Tree-building job
Downloading Newick file
Viewing the tree

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

5:00 pm           Day 1 Adjourn

Wednesday, November 15, 2017

9:00 am           BLAST at PATRIC
Choosing BLAST database
Adjusting parameters
Submitting BLAST job
Downstream analysis of BLAST results

9:45 am           Similar Genome Finder service
Uploading genome sequence
Submitting job
Viewing results

10:00 am         Break

10:15 am         RNA-Seq Pipeline, Downloading Data into PATRIC and Differential Expression
Uploading RNA-seq data
Selecting genomes and mapping
Downloading and using data in PATRIC

11:15 am         Expression Import Service
Uploading data
Identifying reference genomes
Submitting import job
Monitoring job progress

12:00 pm         Lunch

1:00 pm           Comparative Transcriptomics: Exploring public expression data and private data in PATRIC
Locating expression import job
Exploring public gene expression in datasets available in PATRIC
Manipulating expression filter
Manipulating heatmap
Expression and correlation for specific genes in PATRIC

2:00 pm           SNP and MNP Variation service
Uploading reads data
Selecting genomes and mapping
Downloading and using data in PATRIC

3:00 pm           Tn-Seq Service
Uploading data
Running the service
Submitting the Tn-Seq job
Downloading and exploring the data in PATRIC

3:30 pm           Building a Metabolic Model
Building metabolic reconstruction, FBA model construction
Analyzing media types, gap filling, growth, predicting essential genes, knock outs, etc.
Comparing models of genomes

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

5:00 pm           Day 2 Adjourn

Thursday, November 16, 2017

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