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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
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Lab of Mike Lynch
Thank YouOSG Team Rob Quick and Soichi
Hayashi
Questions?
Bill Barnett ([email protected])
Le-Shin Wu ([email protected])
Carrie Ganote ([email protected])
Tom Doak ([email protected])
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 http://omicsmaps.com/
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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
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NCGAS is embedded in Research Technologies
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• 16-nodes, 500GB RAM
• 10TB project space
• Bioinformatics software
• Galaxy instance
• 50TB archive space/userWe 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 STUDYSuspect: Horned Dung BeetleScientific Name: Onthophagus taurus, O. sagittarius, and O. nigriventrisWanted 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 researchWe 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 experienceWe 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
Archive
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
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From our recent NSF survey:
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From our recent NSF survey:
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From our recent NSF survey:
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From our recent NSF survey:
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From our recent NSF survey:
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From our recent NSF survey:
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From our recent NSF survey: