iPlant Genomics in Education Workshop @ University of Alaska, Anchorage
Date and Time
|October 30 2012||9:00 AM - 5:00 PM (Room TBD)|
|October 31 2012||9:00 AM - 5:00 PM (Room TBD)|
Jason Williams: email@example.com
This free 2-day workshop helps college faculty integrate genome analysis into courses and student research projects. The workshop features resources produced by the iPlant Collaborative, a NSF-funded project to develop a computer infrastructure for plant research (www.iplantcollaborative.org). Instruction, workshop materials, lunches, and a $100 stipend are provided by NSF grant funding.
Genomics in Education focuses on DNA Subway (dnasubway.iplantcollaborative.org), an easy-to-use interface that introduces students to bioinformatics analysis and provides an entry point to other research-grade tools. The Red Line assembles mathematical and biological evidence for gene structure and function. The Yellow Line identifies related genes in sequenced genomes. The Blue Line integrates DNA barcode information from wet lab experiments to identify organisms and construct phylogenetic trees.
Day 1: The workshop beings with an introduction to key concepts and challenges of modern genomics, and bioinformatics methods for predicting and annotating genes. Red Line: Use gene predictions and biological evidence to create gene models. Blue Line: Learn about DNA barcoding, and extract DNA from plant samples.
Day 2: Red Line: Prospect for genes and assemble gene models in up to 150 kilobases of raw DNA sequence. Compare gene models with community annotations, and learn about resources available for student annotation projects. Yellow Line: Identify gene and transposon families in different plant genomes. Blue Line: Amplify the barcode region of the chloroplast genome by PCR and send it out for DNA sequencing. (Participant barcode results are available for analysis in 48 hours).
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
We have additional travel funds for individuals who are US citizens/permanent residents; participants from groups underrepresented in the life-sciences, or those who impact these groups, are especially encouraged to apply.
Faculty who are members of AISES traveling to the 2012 national conference will be provided with additional stipends to cover the cost of travel to Anchorage. Additionally, one night's hotel accomidation will be provided. Be sure to register for the AISES national confrence at: www.aises.org/nationalconference
Tuesday, October 30th, 2012
|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|
Wednesday, October 31st, 2012
|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||Classroom planning and review|
|4:30 PM - 5:00 PM||Evaluation, Closure|