IGS Genomics Training Workshop

Overview

The Institute for Genome Sciences at the University of Maryland School of Medicine in Baltimore, Maryland is hosting a 4-day workshop that will provide detailed instruction in the areas of genome sequencing, annotation, and analysis.

The course is designed to be modular in nature so that attendees can choose to attend only the portions of the workshop that they are interested in.

Schedule of topics

Tentative Schedule - subject to change at this point, will be finalized at least one month prior to the start of the workshop

Day 1

Genome Sequencing

  • Whole genome/metagenome shotgun sequencing
  • Genome assembly and closure
  • Review of sequencing technologies outlining strengths and weaknesses of each
  • Hands-on assembly exercises

Day 2

Prokaryotic Gene Finding and Curation

  • Resolving false positives, false negatives

Eukaryotic Gene Finding and Curation

  • Combining information from multiple sources

Protein Functional Annotation (Part 1)

  • Sequence-Based Searches
    • HMM searches
    • BLAST and Smith-Waterman based pairwise search tool BER (Blast_extend_repraze)
    • Assorted motif tools
  • Automatic Functional Annotation
  • Evidence Evaluation and the assignment of annotations to proteins

Gene Ontology system

  • Overview of the GO and structure of the ontologies
  • Annotating with the GO

Day 3

Protein Functional Annotation (Part 2)

Hands-On manual curation with Manatee

  • Manatee demo
  • Annotation exercises

Metagenomics (Part 1)

  • Introduction to metagenomics
  • 16s Ribosomal RNA analysis
  • Whole metagenome analysis

Day 4

Metagenomics (Part 2)

  • Intro to the Human Microbiome Project (HMP)
  • Integrated Microbial Genomes, img/m, img/hmp

Data structures and Pipelines

  • Underlaying chado database structure
  • Basic querying
  • Ergatis/Workflow pipeline management systems
  • Running your own pipeline

Dates and Times

The following courses are scheduled:

  • January 12 - 15, 2010 (waiting list only)
  • April 20 - 23, 2010
  • June 29 - July 2, 2010
  • November in conjunction with the Metagenomics 2010 conference (yet to be scheduled)

Logistics

Location

The course will be held on the University of Maryland Baltimore campus in the BioParkII building at 801 W. Baltimore St. Baltimore, MD 21201. A computer will be provided for your use during the workshop.

Google Maps

Driving directions

Can be found here:

http://www.igs.umaryland.edu/about_directions.php

Parking is available for $9.00 per day in a garage at the corner of W. Baltimore and Poppleton, this is about 1 block from our building.

Airports

The closest airport is Baltimore Washington International Thurgood Marshall Airport (BWI). Other airports in the region (1 - 1.5 hours away) are Dulles and Reagan National.

Train

Baltimore is served by Amtrak and MARC train service.

Lodging

Follow this link to find information on nearby hotels that offer discounted rates for those visiting the University of Maryland, you must mention that you are visiting the University of Maryland to get the discounted rate:

http://www.fincsvc.umaryland.edu/travel/hotels.cfm

Schedule

The workshop will run from 9:00 AM to 5:00 PM each day, with a one hour break for lunch. There are local restaurants where you can get lunch for around $10.00.

How to register

Registration is easy - simply click here and fill out the form.

Questions?

Please send any questions to Michelle (mgiglio AT som.umaryland.edu)