Providing National Cyberinfrastructure to Biologists, esp. Genomicists. William K. Barnett, Ph.D. (Director) Thomas G. Doak (Manager & Domain Biologist) National Center for Genome Analysis Support

2 Lab of Mike Lynch

Thank You OSG Team Rob Quick and Soichi Hayashi Questions? Bill Barnett Le-Shin Wu Carrie Ganote Tom Doak

An outline: The science and research NCGAS addresses What tools and infrastructure NCGAS provides to researchers What is the near to mid-term future of bioinformatics research

Genomics Proteomics Transcriptomics MetaGenomics MetaProteomics MetaTranscriptomics ‘omics is expanding to include everything then Population Genomics, etc. ….

Cost per Genome

03/23/2015

8

Making it easier for Biologists Web interface to NCGAS resources Supports many bioinformatics tools Available for both research and instruction. Common Rare Computational Skills LOW HIGH

Researchers must balance cost, ease, and availability.

NCGAS’s primary goals: Provide bioinformatics expertise Maintain a curated set applications Provide access to HPC resources, esp. large- memory clusters = Mason Build Galaxy instances for our software Pursue out-reach to biologists

NCGAS is embedded in Research Technologies 12

NCGAS is embedded in Research Technologies 13

16-nodes, 500GB RAM 10TB project space Bioinformatics software Galaxy instance 50TB archive space/user We ask that you acknowledge our grant in any published work that uses our resources. Collaborations and authorship are requested for intellectual contributions. THE FACTS The fine print

Mason and NCGAS use over time Users

Mason Use

CASE STUDY Suspect: Horned Dung Beetle Scientific Name: Onthophagus taurus, O. sagittarius, and O. nigriventris Wanted for: Nutrition, metabolism, and horn development. Warning! Subject may be armed with horns which “vary in size, number, position on the body, and degree of sexual dimorphism”. Rapidly evolving genes in three closely related species may be implicated in the diversity of these structures. Suspects’ genomes are under current investigation for strong signals of selection. PI: Melissa Pespeni (lab of Armin Moczek)

Our role in Melissa’s research We recommended assembly procedures and Unix commands – when and how to concatenate data sets together to retrieve the desired information We wrote customized scripts to get the data in the format required by the programs requested We troubleshot issues with the system that were beyond user experience We assisted with the data moving process and advised steps to address data corruption and failures We added new users to project and brought them up to speed on the project and on Unix …With a smile

GALAXY.NCGAS.ORG Model Virtual box hosting Galaxy.ncgas.org The host for each tool is configured individually Quarry Mason Data Capacitor Archiv e NCGAS establishes tools, hardens them, and moves them into production. Custom Galaxy tools can be made for moving data Individual projects can get duplicate boxes – provided they support it themselves. Policies on the DC guarantee that untouched data is removed with time.

Simplify this!

From our recent NSF survey:

From our NSF survey: “The biggest impediment to discovery by biologists is the need to rely on others with knowledge of impenetrable systems and obscure acronyms to process and interpret data. Don't know how to fix this, but on some level user friendly platforms programs like Geneious more than make up for their lack of power by providing an intuitive platform that encourages free exploration and experimentation with data.”

The end…

Mason Use

27 From our recent NSF survey:

28 From our recent NSF survey:

29 From our recent NSF survey:

30 From our recent NSF survey:

31 From our recent NSF survey:

32 From our recent NSF survey:

33 From our recent NSF survey: