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.

The Genomics Education PartnershipSarah Elgin

Use comparative genomics to learn more about chromatin domains in Drosophila genomes:

- improve sequence, annotate, analyze - dot chromosomes (F; heterochromatic)- comparison region (D; euchromatic)

Our GEP research goal:

FlyBase: http://flybase.org

Reference

Status

Completed

Annotation

Sequence Improvement

New Project(motif finding)

D. biarmipes

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.

Curriculum Question

y = axb

No box:Derive the math,

refine the algorithm

How can we help students understand the mathematics or algorithm that underlies a bioinformatics tool?

Glass box:Analyze the math,

Model the relationships

y = axb

Black box:Hide the math

Give enough math to demystify the algorithm & relate it to key biological concepts

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 Biotech 22:1315–6)Anton Weisstein, Truman State University MO

• 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]

A bioinformatics course for biologists?

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

The Genomics Workflow

Public “draft” genomes

Divide into overlapping student projects(~40kb)

Sequence and assembly improvement

Collect projects, compare and verify final consensus sequence

Evidence-based gene annotation

Collect projects, compare and confirm annotations

Reassemble into high quality annotated sequence

Analyze and publish results

Sequence Improvement

Annotation

http://gep.wustl.edu

Students learn to use a UCSC genomebrowser, BLAST, FlyBase,Clustal, others.Students present findings at local meetings;GEP publishes as group.

9

• 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.

Goals:

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.

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.

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.

Phage Bioinformatics students:

Angelica group organizes their workflow… GBrowseDNA Master (Roger Hendrix)BLASTClustalPhamerator (Steve Cresawn)