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GENOME CONSORTIUM ON ACTIVE TEACHING USING NEXT-GENERATION SEQUENCINGVince Buonaccorsi
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HHMI award to Juniata college
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NSF RCN-UBE
Broad Goals Workshop Student Presentations
Leadership and Technology Support
Increase network participation and disseminate to other regions X
Nurture sense of community among young scientists and
educatorsX X
Support network communication, coordination, and sharing of
resourcesX
Specific Objectives
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HHMI COMPUTER CLUSTER SPECS
One Master Node Processors AMD Opteron Eight-Core 16 Cores per Master Node 2 16Gb RAM per Master Node Hard Drive RAID Edition 3TB 6Gb/s Hard Drive, 7200RPM Operating System CenTOS 1
Four Compute Nodes Processors AMD Opteron 32 Cores per Compute Node RAM 8GB 128Gb Ram per Compute Node Hard Drive RAID Edition 500GB 6Gb/s Hard Drive
Cooling Solution Rack 42U Rack Cabinet Managed for Proper Cabinet AirFlow Cooling 12,000 - BTU External Chilling Unit Venting Duct Kit for venting into CRAC / HVAC air return system
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Change through workshops
Research intensive (Penn State) and PUI faculty
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Change through workshops
Research intensive (Penn State) and PUI faculty
EducationalModules
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Change through workshops
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Who is GCAT-SEEK?
MSI14%
Non MSI86%
MSI Institions
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GCAT-SEEK: Nextgen Apps of interest
Eukaryotic Genomics
26%
Bacterial Genomics
18%Metagenomics20%
Transcriptomics36%
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GCAT-SEEK: Organismal Interests
Animalia41%
Archaea2%
Bacteria16%
Fungi 13%
Plantae28%
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GCAT-SEEK: Mainly Small PUIs
0
5
10
15
20
25
30
35
1-1000 1001-5000 5001-10000 10001-20000 20001-30000
Freq
uenc
y
Number of Students
Number of undergraduates at school
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GCAT-SEEK: Low technical experience
05
101520253035
1 2 3 4 5
Freq
uenc
y
Low High
Perl or Python Proficiency
05
1015202530
0 1-5 6-10 11-15 16-20 21-25
Freq
uenc
yNumber of NextGen Data Sets
Analyzed
0
5
10
15
20
25
1 2 3 4 5
Freq
uenc
y
Low High
Linux Proficiency
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GCAT-SEEK: High teaching experience
0
2
4
6
8
10
12
0 1-5 6-10 11-15 16-20 21-25 26-30 31-40
Freq
uenc
y
Years Teaching
Undergraduate Teaching Experience
051015202530
1-5 6-10 11-15
Freq
uenc
y
Years in GCAT
Years in GCAT
0
5
10
15
1 2 3 4 5
Freq
uenc
y
Low High
Familiarity with Assessment Literature
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Merits and Impacts of Network Community of 155 enthusiastic biologists, primarily
teachers from >110 colleges and universities Intellectual synergies on exptal design,
bioinformatics approach, pedagogy & assessment Discounted runs, software, hardware Dissemination of data, pedagogic, assessment
modules Outreach to MSIs Database of barcoded metagenomic primers Student Impact in Year 1: 28 research students, 95
students in labs
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Workshop: Participant Profile
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Workshop Facilitators
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Misc. DetailsMeals: hereCoffee and snacks: meals, lounges downstairsEvening sessions: hereSocials: Pheasant loungeBreakout Rooms: DownstairsQuestions?
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EUKARYOTIC GENOMICS BREAKOUTVince Buonaccorsi
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Eukaryotic genomics breakout Content
Data processing Assembly Genome
Characterization Repeats Gene number
Gene Annotation Ortholog ID Whole genome
alignment
Variant ID Platforms
HHMI Cluster Virtual boxes
Linux applications on personal computers
Galaxy web Amazon EC2
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GCAT-SEEK Sequencing Cores
Founding Genome Core Facility Penn State
Coordinated all 2011runs Advised RNAseq runs 2013 Advised & coordinated euk/prok genomic runs for 2013 GCAT-SEEK workshop presenters
Affiliated Genome Core Facilities Ohio University
In-house prices on Ion Torrent 318 runs Indiana University, Bloomington
In-house prices on Illumina HiSeq runs