GENOME CONSORTIUM ON ACTIVE TEACHING USING NEXT-GENERATION SEQUENCING Vince Buonaccorsi.

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Vince Buonaccorsi Associate Professor of Biology Juniata College.

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Presentation transcript:

GENOME CONSORTIUM ON ACTIVE TEACHING USING NEXT-GENERATION SEQUENCING Vince Buonaccorsi

HHMI award to Juniata college

NSF RCN-UBE

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 Educational Modules

Change through workshops

Who is GCAT-SEEK?

GCAT-SEEK: Nextgen Apps of interest

GCAT-SEEK: Organismal Interests

GCAT-SEEK: Mainly Small PUIs

GCAT-SEEK: Low technical experience

GCAT-SEEK: High teaching experience

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: here Coffee and snacks: meals, lounges downstairs Evening sessions: here Socials: Pheasant lounge Breakout Rooms: Downstairs Questions?

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