Bioinformatics at National

University: the GEP experience

Ana Maria BarralDept. Mathematics & Natural Sciences

COLS

This presentation• Part 1 General aspects

o What is Bioinformatics (very simple)o What is GEP?o How does it work?o GEP for beginning students: spread the word!o NU experience

• Part 2 Technical aspectso The scientific problem in GEPo Drosophila species and sequenceso Workflowo Nu experience

Part 1

General aspects

What is Bioinformatics?

• Interdisciplinary field• Uses mathematical and

computational approaches to analyze biological data

• One of the most growing career fields (technician to Ph.D. level)

DNA sequencing advances and the increase in

computational power have largely increased

the amount of data available & decrease the

cost of sequencing

What is GEP?• Collaboration between a growing

number of primarily undergraduate institutions and the Biology Dept and Genome Center of Washington University in St. Louis.

• Project leader Sally Elgin• Core group of collaborators and support

staff• Funded by HHMI & NSF (2014 and on)• Research project related to the

genetics of the fruitfly (Drosophila)• More fruitfly species are sequenced:

comparative genomics

Year joined:

2006

2007

2008

2009

2010

2011

2012

2013

GEP Members, 2014

Slide by S.E.

Currently ~100 faculty partners from > 110 colleges & universities; last year ~1300 students enrolled in GEP-associated courses.

Of 107 schools surveyed in 2013:• Public (57), private (50)• Small (13 schools < 2000), large (35 schools >

10,000)• 65 BA only, 20 schools award MA’s, 5 award

PhD’s• Life science majors range from 2% to 13%

• At 15 schools > 80% of students live on campus• At 25 schools > 80% of students commute• At 8 schools > 30% are non-traditional students• At 10 schools > 30% of students are first

generation• At 27 schools > 40% are minority students

This suggests that the approach is broadly applicable.Slide by S.E.

GEP: great diversity in participating schools

How does GEP work?• Requirement: computers and internet access• Partners receive onsite training (until 2014 fully

covered, future depends on funding)• Partners implement the curriculum (all materials

available)• Students download and work with DNA sequences,

which they submit to WU for quality control• Students complete pre- and post-course surveys and

quizzes• Partners report back, and support GEP in different

ways (funding, work on specific areas, etc.)• Active partners & students become publication

coauthors (latest paper has >500 student & >50 faculty coauthors)

• Part of the BS Biology sequence, follows Genetics

• 8 week lecture + lab, GEP implemented for lab

• Total of 10 class meetings, 4.5 hours each (lab).

• Although 10-12 hours of annotation were planned, total hours spent in-class were 20-25 hours, plus student individual time.

• Lecture included a scaffolded written project on a Drosophila gene to support the GEP project.

GEP in a Molecular Biology lab course

(BIO407A)

The bad…• No “TA” (peer instructor) for a class of 12• Student complaints:

o Instructions confusing o Tutorials difficult and wordyo Excessive workloado Too much emphasis on annotation within the course material

• “So are we working for free for Washington University?” Lack of clarity about research and project ownership.

• Interestingly, end-of-course survey scores were better for lab (GEP) than for lecture!

• Student preparation and effort directly proportional to annotation success (systematic issue w/non-traditional students)

The Good• Student engagement was palpable.• Student surveys scored high (>4) for critical

thinking, deeper knowledge of the material, apply the knowledge to real life.

• “It was refreshing to have a professor give me the opportunity to work on such a meaningful task like the WU project. Even though it was extremely challenging at times, it was nice to know that I was working for something more than just a grade.”

Current project: GEP for beginning students

• GEP just received new funding by NSF• Important goal: to develop curriculum

to use GEP for beginning students (ongoing)

• Particularly desirable: community college students (only 4 partners are from CCs)

• Due to decreased funding, local/regional support/collaborations will be more important.

• Please spread the word to your connections in CCs!

• NU could be a “hub” in CA

Part 2

Technical/scientific aspects

Use comparative genomics to learn more about heterochromatic domains, analyzing the dot chromosomes and a control euchromatic region of Drosophila genomes

GEP research goal:

FlyBase: http://flybase.org

Reference

Status

Completed

Annotation

Sequence Improvement

New Project

Slide by S.E

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.

Annotation & Finishing

• Annotation only requires computers & internet access

• Uses mainly UCSC genome browser, Blast, & FlyBase.

• Students compare the novel sequence with the D. melanogaster sequence, and evaluate the existing predictions.

• Finishing requires Consed (Unix based, best run on Macs)

• Students analyze sequences and help determining the consensus sequence.

NU Annotation projects

• “I know that the projects your students submitted look pretty good - thoroughly done - although there are a couple of splice sites that may end up being changed.” Sally Elgin.

Finishing

Different Modes of Participation• Introductory labs using sequence data, web tools

• Using computer-based protocols and selected prepared genome data sets to challenge students to analyze and annotate a previously studied or novel sequence – this is used for short (10 hr) teaching modules (Cal State, Amherst).

• Working with the GEP in annotating selected portions of a genome in a collaborative research project – commonly used

• Generating DNA sequencing reactions with one's own material to be read by WU sequencing machines, with the output returned to the students for analysis – rarely used

Working with the GEP in finishing selected portions of a genome in a collaborative research project – used by ~15%

Slide by S.E.

Thank you!