GENOME CONSORTIUM ON ACTIVE TEACHING USING NEXT-GENERATION SEQUENCING

Vince Buonaccorsi

HHMI award to Juniata college

NSF RCN-UBE

Broad Goals WorkshopStudent

PresentationsLeadership 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

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

Change through workshops

Research intensive (Penn State) and PUI faculty

Change through workshops

Research intensive (Penn State) and PUI faculty

EducationalModules

Change through workshops

Who is GCAT-SEEK?

MSI14%

Non MSI86%

MSI Institions

GCAT-SEEK: Nextgen Apps of interest

Eukaryotic Genomics

26%

Bacterial Genomics

18%Metagenomics20%

Transcriptomics36%

GCAT-SEEK: Organismal Interests

Animalia41%

Archaea2%

Bacteria16%

Fungi 13%

Plantae28%

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

GCAT-SEEK: Low technical experience

05

101520253035

1 2 3 4 5

Fre

qu

ency

Low High

Perl or Python Proficiency

05

1015202530

0 1-5 6-10 11-15 16-20 21-25

Fre

qu

ency

Number of NextGen Data Sets Analyzed

0

5

10

15

20

25

1 2 3 4 5

Fre

qu

ency

Low High

Linux Proficiency

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

Fre

qu

ency

Years Teaching

Undergraduate Teaching Experience

051015202530

1-5 6-10 11-15

Fre

qu

ency

Years in GCAT

Years in GCAT

0

5

10

15

1 2 3 4 5

Fre

qu

ency

Low High

Familiarity with Assessment Literature

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

Workshop: Participant Profile

Workshop Facilitators

Misc. Details

Meals: hereCoffee and snacks: meals, lounges downstairsEvening sessions: hereSocials: Pheasant loungeBreakout Rooms: DownstairsQuestions?

EUKARYOTIC GENOMICS BREAKOUT

Vince Buonaccorsi

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

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