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

The PATRIC/RAST teams will be offering a tutorial on 2017-August 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 to India Gordon at <rast-workshop@mcs.anl.gov>.

NOTE: All workshop attendees must also separately fill out the “Argonne Visitor Request” form at: <https://webapps.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 <igordon@anl.gov> as your “Sponsor’s e-mail address.”

LOCATION

Argonne National Laboratory

Building 240, Room 1404/1405

Argonne, IL 60439

DRAFT AGENDA  (PDF version)

Monday, August 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

Tuesday, August 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 

Wednesday, August 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