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iPlant Genomics in Education Workshop - Prairie View A&M University; September 26-27th, 2013

Date and Time

September 26 2013 9:00 AM - 5:00 PM (Room TBD)
September 27 2013 9:00 AM - 5:00 PM (Room TBD)

Location

Prairie View A&M University

Primary Contact

Jason Williams: williams@cshl.edu

Details

This free workshop empowers college faculty to integrate modern methods for genome analysis into courses and student research projects. All the resources presented in the workshop are produced by the iPlant Collaborative, a NSF-funded project to develop a computer infrastructure for plant research (www.iplantcollaborative.org). Instruction, workshop materials, and lunches are provided by NSF grant funding.

Genomics in Education focuses on DNA Subway, a website that introduces students to sophisticated bioinformatics though an easy-to-use interface. The Red Line assembles mathematical and biological evidence for gene structure and function. The Yellow Line identifies related genes in sequenced genomes. Blue Line integrates DNA barcode information from wet lab experiments to identify organisms, construct phylogenetic trees, and publish sequence data to the scientific community. The Green Line introduces high-throughput sequencing through the investigation of an RNA-Seq dataset for differential expression.

Who should attend?

Biology educators working with undergraduate students are our primary focus. However, educators working with advanced high school students, or graduate students and post-docs with teaching responsibilities will also benefit from attending.

What will we do at the workshop?

The majority of the workshop will focus on using the DNA Subway website to analyze DNA sequence with a variety of outcomes. We will understand how to determine the structure and function of genes, and learn more about the genomes of organisms around us. We will also do a hands-on DNA extraction (bring a leaf from your favorite plant) and use DNA Subway to identify the organism by DNA sequencing.

Some examples of the how DNA Subway has been used for student projects can be found here:

What do I need to bring?

Please bring a Wi-Fi enabled laptop (additional suggestions for updates will be provided before you come). Lunches will be provided, but participants are responsible for all travel costs.

Key concepts embodied by the lab and bioinformatics work include:

  • DNA sequence is information.
  • Gene annotation adds meaning to DNA sequence.
  • A genome is more than protein coding genes.
  • Genomes are complex and dynamic.
  • The concept of a gene and a species continue to evolve.
  • DNA barcoding bridges molecular genetics, evolution, and conservation biology

Agenda

Thursday, September 26th, 2013

Time Description
9:00 AM - 9:15 AM
Welcome, Logistics
9:15 AM - 10:00 AM
Introductions
10:00 AM - 10:30 AM
iPlant Collaborative, Workshop Objectives, DNA Subway Tour
10:30 AM - 10:45 AM
Break
10:45 AM - 11:15 AM
Using DNA Subway to Teach Concepts in Molecular Biology
11:15 AM - 12:00 PM
Setting up Projects for Annotation – Red Line
12:00 PM - 1:00 PM
Lunch
1:00 PM - 1:15 PM
DNA Barcoding - DNA Isolation
1:15 PM - 1:30 PM
Mini-Seminar: DNA Barcoding
1:30 PM - 2:45 PM
DNA Barcoding (continued)
2:45 PM - 3:00 PM
Break
3:00 PM - 3:15 PM
Mini Seminar: Evidence Based Gene Modeling
3:15 PM - 4:45 PM
Gene Annotation I
4:45 PM - 5:00 PM
Mini-Seminar: Alternative Splicing

Friday, September 27th, 2013

Time Description
9:00 AM - 9:30 AM
Mini-Seminar: Transposons
9:30 AM - 10:15 AM
Genome Prospecting: Transposon Sleuthing – Yellow Line
10:15 AM - 10:30 AM
Break
10:30 AM - 11:30 AM
Gene Annotation II
11:30 AM - 12:00 PM
DNA Barcoding (PCR)
12:00 PM - 1:30 PM
Lunch
1:30 PM - 2:30 PM
DNA Barcoding - Blue Line
2:30 PM - 2:45 PM
Break
2:45 PM - 3:45 PM
DNA Barcoding - Electrophoresis and Sequencing prep
3:45 PM - 4:30 PM
Differential Expression of RNA-Seq Data - Green Line
4:30 PM - 5:00 PM
Evaluation, Closure