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