The Next Big Thing Collaborations in the Life Sciences
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Transcript of The Next Big Thing Collaborations in the Life Sciences
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The Next Big ThingCOLLABORATIONS IN THE LIFE SCIENCES
Gordon K SpringerUniversity of Missouri
Internet2 Spring Member MeetingApril 24, 2012
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Developing a 100G TestBedfor Life Science Collaborations
Taking advantage of existing UM/SURA dark fiber to create a research 100G pathway from St Louis to Kansas City via Columbia along Interstate 70
Using InCommon Federated Identities for authentication via Shibboleth; authorizations occur via an autonomous Entitlement Server to provide fine-grained authorizations to/from service providers
Developing distributed resource sharing by mapping needs to resources eligible for assignment depending on geography and resource availability
At 100G some distributed computing latency issues can likely be overcome
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Problem Set
High-Throughput Sequencing is producing enormous quantities of data; needing a storage infrastructure as a private cloud
Need to provision collecting, analyzing and using resources according to demand and includes the processing applications being net-aware
Develop security, measurement and analysis tools to efficiently run at 100G across a regional multi-cluster environment using OpenFlow and other specialized protocols
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High throughput DNA sequencing at MU DNA Core Facility.
Sequence data
analyzed at MU on
high-speed systems.
Patterns of gene expression analyzed with microarrays to reveal mechanisms that contribute to reproduction efficiency.
Improved efficiency, quality and profitability is the goal.
Gene annotations quickly obtained by access to other data-bases through the MU Internet2 high speed network.
Swine female reproductive tissues and embryos are removed at various times of gestation.
Iterate microarray & other experiments to focus on gene discovery.
Where Does the Data Come From?A High-Volume EST Pipeline For
Discovery
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ColKC SLI70
Big Data/Big Science Collaboratory
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The GPN Network
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Grant Writers Professional Development Sessions
University of Missouri System
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UM InterCampusNetwork with 100G Pathway along I70
100G 100G
HtSeqLSC
Internet2
UM Portion of MOREnet
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Multi-Site Sharing
SMP Servers Linux Cluster GPGPUsHPC Storage
Visualization & Display
IBM
H C R U6
IBM
H C R U6
IBM
H C R U6
IBM
H C R U6
HPC Infiniband Network
Machine Room GbE Network
ProtocolsCIFSNFSHTTPFTPSCP
ManagementCentralAdministrationMonitoringFile Mgmt
AvailabilityData MigrationReplicationBackup
Research Data Store
Campus GbE Network
Instruments (Medical)
Instruments(Core Service)
Instrument(Research)
Lab (Research & Clinical)
Mgmt
OpenFlowAnd
Other Protocols
LOGIN CLOUD
Next-Gen Linux Cluster GPGPUsHPC Storage
Visualization & Display
IBM
H C R U6
IBM
H C R U6
IBM
H C R U6
IBM
H C R U6
HPC Infiniband Network
Machine Room GbE Network
ProtocolsCIFSNFSHTTPFTPSCP
ManagementCentralAdministrationMonitoringFile Mgmt
AvailabilityData MigrationReplicationBackup
Research Data Store
Campus GbE Network
Instruments (Medical)
Instruments(Core Service)
Instrument(Research)
Lab (Research & Clinical)
Mgmt
CLOUD LOGIN
Site A Site B
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Adapted from: The Stanford Clean Slate Program http://cleanslate.stanford.edu
Controller
PC
NetStorage
Storage Cloud
OpenFlow at the packet level
OpenFlow-enabledCommercial Switch
FlowTable
SecureChannel
NormalSoftware
NormalDatapath
NetProcessors
Analysis EnginesUser
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11
Collaborative Framework
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Bridging the Gaps(Some are very Large)
• Data• Processors
•Provider• Authenticate
(InCommon)Analysis
ToolsSharing
AppsNets
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WAYF
Identity Provider Service Provider
IdentityDirectory
Handle Service
AttributeAuthority
SHIRE
SHAR
Resource
Manager
Resource
Attributes
Credentials
Handle
Handle
5
2
34
51
66
13
14
Entitlement Server
Administrative User
Entitlement Client App
10
7
12
Command
YES/NO
Handle
VO Entitlement Command
Credentials8
9
Command
YES/NO
11Using Middleware
Tools for VO Collaboration ES DB
Entitlement Server
User
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User
Service Provider
Entitlement Server
Identity Provider
Page or computational results
1: request by URL or command
2 3
4
5
6uses public key encryption for authentication
and privacy
Simplified Design
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Getting Authenticated
If you belong to a GPN member organization, but do not see your institution in the list,please contact your local GPN representative to request help in authenticating in thisenvironment.
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2/24/2008 16
Entering the VO Environment
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And the story continues …More Data, Resources, People
& Knowledge
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02/14/2007 Grant Writers Professional Development Sessions 18
UMBC
http://umbc.rnet.missouri.edu