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Genome Consortium on Active Teaching using Next-Generation Sequencing

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

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Genome Consortium on Active Teaching using Next-Generation Sequencing

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  1. Genome Consortium on Active Teaching using Next-Generation Sequencing Vince Buonaccorsi

  2. HHMI award to Juniata college

  3. NSF RCN-UBE

  4. 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 CenTOS1 • 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

  5. Change through workshops Research intensive (Penn State) and PUI faculty

  6. Change through workshops Research intensive (Penn State) and PUI faculty Educational Modules

  7. Change through workshops

  8. Who is GCAT-SEEK?

  9. GCAT-SEEK: Nextgen Apps of interest

  10. GCAT-SEEK: Organismal Interests

  11. GCAT-SEEK: Mainly Small PUIs

  12. GCAT-SEEK: Low technical experience

  13. GCAT-SEEK: High teaching experience

  14. 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

  15. Workshop: Participant Profile

  16. Workshop Facilitators

  17. Misc. Details Meals: here Coffee and snacks: meals, lounges downstairs Evening sessions: here Socials: Pheasant lounge Breakout Rooms: Downstairs Questions?

  18. Eukaryotic Genomics breakout Vince Buonaccorsi

  19. 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

  20. 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 IlluminaHiSeq runs

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