hackathon tips&tricks minion_communitymeeting_2015_zaaijer
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@Sophie_Zaaijer Ubiquitous Genomics in the classroom12/03/2015
Ubiquitous Genomics in the classroom Sophie Zaaijer
Dec 2015 Min
ION Sophie Zaaijer Post-doc in Yaniv Erlich’s lab
@Sophie_Zaaijer
@Sophie_Zaaijer Ubiquitous Genomics in the classroom12/03/2015
Diverse group of students
20 Students
@Sophie_Zaaijer Ubiquitous Genomics in the classroom12/03/2015
Outline course
Seminars Hackathons What is DNA
Sequencing technologies
Current applications Application
visions
6 weeks
“Snack to
Sequence”
Analysis pipeline
“CSI Columbia ”
Analysis pipeline
3 weeks 3 weeks
@Sophie_Zaaijer Ubiquitous Genomics in the classroom12/03/2015
Hackathons
1 “Snack to Sequence” – Nanopore Sequencing
– Opportunities portable sequencing
– Interpret data
– Biological relevance
2 “CSI Columbia” – Person identification
– Minimal SNP
– Ethical boundaries
@Sophie_Zaaijer Ubiquitous Genomics in the classroom12/03/2015
Hackathon Challenges
@Sophie_Zaaijer Ubiquitous Genomics in the classroom12/03/2015
1 Spare parts, reagents
2 Test functionality of library
3 Have backup data
4 Software + settings
Hackathon Challenges
@Sophie_Zaaijer Ubiquitous Genomics in the classroom12/03/2015
1 Spare parts, reagents
2 Test functionality of library
3 Have backup data
4 Software + settings
5 Data transfer
Hackathon Challenges
@Sophie_Zaaijer Ubiquitous Genomics in the classroom12/03/2015
Variability in yield
02000400060008000
100001200014000
# Reads
num
ber o
f rea
ds
Hack 1 Hack 2
Hackathon Challenges
@Sophie_Zaaijer Ubiquitous Genomics in the classroom12/03/2015
Planning of a Hackathon
DNA extraction Library prepMinIONs + reagents
Computers
Hackathon
2 days
Experimental plan
Prepare fuel-mixPrep all reagents
1 hr
Seminar
45 min
Pipet practice
15 minDays/Weeks
Fuel
20 min
Prep Pre-seq mixStart Run Start MinKNOW Start Metrichor
30 min
Data transfer
@Sophie_Zaaijer Ubiquitous Genomics in the classroom12/03/2015
From snack to sequence
Samples taken from supermarket
2 ingredients per DNA library 2 ratios
@Sophie_Zaaijer Ubiquitous Genomics in the classroom12/03/2015
Student output : Identify ingredients
@Sophie_Zaaijer Ubiquitous Genomics in the classroom12/03/2015
Student output : Identify ingredients
Group 4
@Sophie_Zaaijer Ubiquitous Genomics in the classroom12/03/2015
• Approach 1: ratio # reads11 min: identification of species >2%62 min: identification of all species with >=1 read3 hours : ratios remained invariant
• Approach 2: Ratio normalized by genome size3.3 hours : ball park ratio 9 hours: ratios remained invariant
• Approach 3: Ratio # bases 1.5 hours : ball park ratio 3.3 hours: ratios remained invariant
Students explore: How fast can we go?
Time
Ratio
Species 1
Species 2
Species 3
?
@Sophie_Zaaijer Ubiquitous Genomics in the classroom12/03/2015
Columbia
@Sophie_Zaaijer Ubiquitous Genomics in the classroom12/03/2015
Student Opinion
• Questionnaire – Before Hackathon – After Hackathon
@Sophie_Zaaijer Ubiquitous Genomics in the classroom12/03/2015
Questionnaire IWhen do you think the real time sequencing will be used to do person identification at borders, instead of passports/drivers
licenses?
@Sophie_Zaaijer Ubiquitous Genomics in the classroom12/03/2015
Questionnaire IIHow much would you pay to use ‘home’
sequencing for health applications?
@Sophie_Zaaijer Ubiquitous Genomics in the classroom12/03/2015
MinION in the classroom - Conclusions:
• MinION is a great tool to teach students genomics.
• 2/3 hours data
• Hackathon day : no extensive wet-lab infrastructure
• Students enjoyed analyzing data they generated
themselves.
• Future Hackathons: student-designed experiments
@Sophie_Zaaijer Ubiquitous Genomics in the classroom12/03/2015
Resources Check out the class website: http://UbiGen.TeamErlich.org/
Acknowledgements
ONT Jim BrayerMichael Micorescu Zoe McDougall
Yaniv Erlich Columbia Students
@Sophie_Zaaijer Ubiquitous Genomics in the classroom12/03/2015