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I hear and I forget. I see and I remember. I do and I understand. - Confucius

The Genomics Education Partnership Sarah Elgin. I hear and I forget. I see and I remember. I do and I understand. - Confucius PCAST recommendation #2: “ Advocate and provide support for replacing standard laboratory courses with discovery-based research courses. ”

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I hear and I forget. I see and I remember. I do and I understand. - Confucius

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  1. The Genomics Education Partnership Sarah Elgin I hear and I forget. I see and I remember. I do and I understand. - Confucius PCAST recommendation #2: “Advocate and provide support for replacing standard laboratory courses with discovery-based research courses.” Bioinformatics (genomics) will help us meet this challenge.

  2. Our GEP research goal: Use comparative genomics to learn more about chromatin domains in Drosophila genomes: - improve sequence, annotate, analyze • dot chromosomes (F; heterochromatic) • comparison region (D; euchromatic) Status D. biarmipes Reference Completed Annotation Sequence Improvement New Project (motif finding) FlyBase: http://flybase.org

  3. Annotation challenge: Create gene models from evidence: sequence similarity, computational predictions, RNA-Seq, etc. (local UCSC Browser) Improved Sequence Sequence Homology Gene Predictions RNA-Seq, TopHat, Cufflinks Repeats Students learn to use a UCSC genome browser, BLAST, FlyBase, Clustal, other data bases and tools.

  4. y = axb y = axb Curriculum Question How can we help students understand the mathematics or algorithm that underlies a bioinformatics tool? Black box: Hide the math Glass box: Analyze the math, Model the relationships No box: Derive the math, refine the algorithm Give enough math to demystify the algorithm & relate it to key biological concepts

  5. Interactive Excel Tool for Exploring Hidden Markov Models: Exon to Intron Transition Adjust probabilities to model specific system Excel computes likelihood of indiv. splice site positions Based on Eddy 2004 (Nat Biotech22:1315–6) Anton Weisstein, Truman State University MO

  6. A bioinformatics course for biologists? • Becoming intelligent users of bioinformatics tools (understanding algorithms, key parameters; command line manipulation) • Analysis and data mining in complex eukaryotic genomes: new questions, new tools • Metagenomics: interesting questions, needed analytical tools • Analyzing RNA samples, mapping to known genomes (developmental progressions, environmental responses) • Regulatory networks, signaling, patterns of relationships • [Training biology faculty to become bioinformatics faculty]

  7. Science efficacy survey results comparing ~10 hr course (blue) and ~45 hr course (red) with summer-in-the-lab (green) . GEP school SURE 09 Bio

  8. The Genomics Workflow Public “draft” genomes http://gep.wustl.edu Divide into overlapping student projects(~40kb) Annotation Sequence and assembly improvement Evidence-based gene annotation Collect projects, compare and confirm annotations Collect projects, compare and verify final consensus sequence Sequence Improvement Reassemble into high quality annotated sequence Students learn to use a UCSC genome browser, BLAST, FlyBase,Clustal, others. Students present findings at local meetings; GEP publishes as group. Analyze and publish results

  9. Goals: • Integration of genomics into the undergraduate biology curriculum • Integration of research thinking into the academic year curriculum • Advantages of bioinformatics / genomics: • Low laboratory costs (computers, internet connection) • No lab safety issues; open access 24/7 • Large pool of publically accessible raw data • Lends itself to peer instruction • Currently ~100 faculty partners from > 110 colleges & universities; last year ~1300 students enrolled in GEP-associated courses.

  10. Selected student quotes….. • The class was very intellectually challenging for me. It taught me to think in a way that I had never thought before. • The thing that sparked me the most was the fact that I was able to perform the BLAST searches on my own and was able to explain to my instructor what I had done. • It was a great team-building and learning experience. It was independent work, but you were going through the same things as the other students and built camaraderie. • I seriously think this should be the model for all biology courses.

  11. But…more comments from GEP students • I learned to fight through the frustration and eventually figure out the problem. • I guess we learned about genomics through doing the tasks…. it was sort of a self-teaching class…. • Everything we gained from the class…was either found by desperately messing around on the various websites …or by talking with other students. • I know if I could survive this class then I could survive just about anything.

  12. Can it work with freshmen? Yes - Phage Hunters! Graham Hatfull, U Pittsburgh: bacteriophage discovery and genomics for novice scientists Small genomes (50 – 150 kb, ~100 genes), simpler – continuous ORF. Now in use at many institutions, start-up supported by SEA (HHMI). Bioinformatics being introduced into general freshman course at Wash U as an optional lab, 20 contact hrs plus homework.

  13. Phage Bioinformatics students: Angelica group organizes their workflow… GBrowse DNA Master (Roger Hendrix) BLAST Clustal Phamerator (Steve Cresawn)

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