1. JMC CGEMS SUMMER GENOMICS TRAINING WORKSHOPS
Genomics in Education
JMC CGEMS SUMMER GENOMICS TRAINING WORKSHOPS
Jason Williams – Education, Outreach, Training Lead
Cold Spring Harbor Laboratory
@JasonWilliamsNY

2. CyVerse evolution iPlant 2013 CyVerse 2016 Cyberinfrastructure for
Life Sciences
funding renewal
CyVerse 2016
Transforming Science Through Data-Driven Discovery
iPlant 2008
Empowering a
New Plant Biology
2017
2006
public launch
2010
2015

3. Transforming science through data-driven discovery
CyVerse vision
Transforming science through data-driven discovery
More than 40K users, PBs of data, and hundreds of publications, courses, and discoveries

4. What is Cyberinfrastructure?
Data storage
Software
High-performance computing
People
organized into systems that solve problems of size and scope that would not otherwise be solvable.

5. What is Cyberinfrastructure?
Platforms, tools, datasets Storage and compute Training and support

6. Genomics in Education

7. Big data biology – Education and Research
100K fold costs decrease in sequencing
Hand-held sequencers
Drones
Biological sensors
Biology is swimming in data
Image Credits:
Genome sequencing costs:
Oxford nanopore sequencer:
Fitbit:
Agricultural drone:

8. Big data biology – Too fast to keep up?
“Essentially, all models are wrong, but some are useful” – George E.P. Box

9. Big data biology – Too fast to keep up?

10. Big data biology – Too fast to keep up?
1866 – Mendel publishes work on inheritance
1869 – DNA discovered
1915 – Hunt Morgan describes linkage and recombination
1953 – Structure of DNA described
1956 – Human chromosome number determined
1968 – First gene mapped to autosome
1977 – Dideoxy sequencing
1983 – PCR
1986 – Human Genome Project proposed

11. Big data biology – Too fast to keep up?
1993 – First MicroRNAs described
2003 – First ‘Gold Standard’ human genome sequence
2005 – First draft of human haplotype map (HapMap)
2007 – ENCODE project

12. Big data biology – Too fast to keep up?

13. Challenge – bringing students into the fold
Research
Education
Students can work with the same data at the same time and with the same tools as research scientists.
How do scientists share their data and make it publically available?
How do scientists extract maximum value from the datasets they generate?
How can students and educators (who will need to come to grips with data-intensive biology) be brought into the fold?

14. Can you navigate the tools?
What are your challenges in teaching bioinformatics in the classroom?

15. Take the Subway

16. DNA Subway Faculty identified guiding requirements
Classroom friendly bioinformatics
Faculty identified guiding requirements
that shaped the development of CyVerse educational platforms:
Mix lecture and lab – have a wet bench “hook”
Student-scientist partnerships – someone has to care about the data
Co-investigation – projects should potentially lead to publications
Scale – platforms should support projects multiple classrooms can join.

17. DNA Subway Red Line Analyze up to 150 KB of DNA sequence
Red Line: Genome annotation
Red Line
Analyze up to 150 KB of DNA sequence
De novo gene prediction
Construct evidence-based gene models
Visualize genome sequence in browser

18. DNA Subway Yellow Line Analyze DNA or protein sequence
Yellow Line: Genome prospecting
Yellow Line
Analyze DNA or protein sequence
Search plant genomes using TARGeT
Explore gene duplications, transposons, and non-coding sequences not detectable in conventional BLAST searches

19. DNA Subway Blue Line Analyze DNA or protein sequence
Blue Line: DNA barcoding, and phylogenetics
Blue Line
Analyze DNA or protein sequence
Search plant genomes using TARGeT
Explore gene duplications, transposons, and non-coding sequences not detectable in conventional BLAST searches

20. DNA Subway Green Line Examine RNA-Seq data for differential expression
Green Line: Transcriptome analysis
Green Line
Examine RNA-Seq data for differential
expression
Use High-performance computing to analyze complete datasets
Generate lists of genes and fold-changes; add results to Red Line projects

21. CyVerse Executive Team