clemson nextnet sdn use cases for life sciences research kuang -ching “ kc ” wang...
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Clemson NextNet SDN Use Cases for Life Sciences Research Kuang -Ching “ KC ” Wang Associate Professor Clemson University Sponsored by NSF grant OCI‐1245936. Clemson NextNet: A NSF CC-NIE Project. Objectives: Direct access to I2 100G Innovation Platform - PowerPoint PPT PresentationTRANSCRIPT
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Clemson NextNet
SDN Use Cases for Life Sciences Research
Kuang-Ching “KC” WangAssociate ProfessorClemson University
Sponsored by NSF grant OCI‐1245936KC Wang Clemson University 1July 17 2013
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Clemson NextNet: A NSF CC-NIE Project
July 17 2013 2KC Wang Clemson University
Objectives:• Direct access to I2
100G Innovation Platform
• Science DMZ from anywhere, w/o manual plumbing
• Campus production,end-to-end support
• Flexible, optimized10~40G access to resources on campus and other universities
• Software defined network (SDN)
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What is the Fuss About SDN?
KC Wang Clemson University July 17 2013 3
NetworkResearchers:
Industry:Traditional network gettinging unmanageable (not about bandwidth)!
Traditional Network SDN
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What Do Our (Life Sciences) Folks Need?
KC Wang Clemson University July 17 2013 4
Real-time medical imaging
Two Clemson life sciences researchers in attendance today:• Alex Feltus
– Associate Professor in Genetics & Biochemistry
– Faculty Consultant in Clemson University Genomics Institute
– Research: Rapid crop design with massive gene interaction networks
• David Kwartowitz– Assistant Professor in
Bioengineering– Research: Rapid processing stereo
laparoscopic data for real-time pre- and intra-surgery support
PalmettoHPC
Cluster
DataStore
N…
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The Feltus Lab Builds Massive Gene Interaction Networks Using RNA Expression Profiles From Next-Generation Sequence (NGS) and Microarray Experiments.
Rice (Oryza sativa)
Goal: Rapidly design new crop varieties for a specific environment including “old” environments with a changed climate…
Personalized Agriculture
Slide prepared by Alex FeltusKC Wang Clemson University July 17 2013 5
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Massive amounts of DNA/RNA/Genetic Data in Databases
1.64 Quadrillion base pairs in 5 yrs!
http://www.ncbi.nlm.nih.gov/Traces/sra/ Slide prepared by Alex FeltusKC Wang Clemson University July 17 2013 6
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A NGS Biomarker Example Datasets
5.7G Sample_Feltus1_L006_R1.cat.fastq5.7G Sample_Feltus1_L006_R2.cat.fastq5.8G Sample_Feltus1_L007_R1.cat.fastq5.8G Sample_Feltus1_L007_R2.cat.fastq6.7G Sample_Feltus2_L006_R1.cat.fastq6.7G Sample_Feltus2_L006_R2.cat.fastq6.8G Sample_Feltus2_L007_R1.cat.fastq6.8G Sample_Feltus2_L007_R2.cat.fastq6.5G Sample_Feltus3_L006_R1.cat.fastq6.5G Sample_Feltus3_L006_R2.cat.fastq6.6G Sample_Feltus3_L007_R1.cat.fastq6.6G Sample_Feltus3_L007_R2.cat.fastq7.3G Sample_Feltus4_L006_R1.cat.fastq7.3G Sample_Feltus4_L006_R2.cat.fastq7.4G Sample_Feltus4_L007_R1.cat.fastq7.4G Sample_Feltus4_L007_R2.cat.fastq5.6G Sample_Feltus5_L006_R1.cat.fastq5.6G Sample_Feltus5_L006_R2.cat.fastq5.7G Sample_Feltus5_L007_R1.cat.fastq5.7G Sample_Feltus5_L007_R2.cat.fastq8.8G Sample_Feltus6_L006_R1.cat.fastq8.8G Sample_Feltus6_L006_R2.cat.fastq8.9G Sample_Feltus6_L007_R1.cat.fastq8.9G Sample_Feltus6_L007_R2.cat.fastq
2.4G Sample_Feltus1_L007_R1.MERGED.BAM2.4G Sample_Feltus1_L007_R1.MERGED.BAM2.7G Sample_Feltus2_L006_R1.MERGED.BAM2.7G Sample_Feltus2_L007_R1.MERGED.BAM2.6G Sample_Feltus3_L006_R1.MERGED.BAM2.6G Sample_Feltus3_L007_R1.MERGED.BAM3.0G Sample_Feltus4_L006_R1.MERGED.BAM3.0G Sample_Feltus4_L007_R1.MERGED.BAM2.2G Sample_Feltus5_L006_R1.MERGED.BAM2.2G Sample_Feltus5_L006_R1.MERGED.BAM2.9G Sample_Feltus6_L006_R1.MERGED.BAM2.9G Sample_Feltus6_L007_R1.MERGED.BAM
6 RNA Samples in Duplicate163.6 GB (raw) + 31.8 GB (processed) =195.4 GB of critical data files(<6 hours to process on cluster)
Does not include: Intermediate processing filesReference genome (0.72 GB)
RAW DATA (uncompressed) PROCESSED DATA (compressed)
Slide prepared by Alex FeltusKC Wang Clemson University July 17 2013 7
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The CUTTERS (Kwartowitz) lab is working to enable remote processing of stereo laparoscopic data for real-time feedback with surgical robot systems
on partner sites (Vanderbilt, Mayo Clinic)
KC Wang Clemson University 8July 17 2013
Clemson, SC
Vanderbilt, TN
Mayo Clinic, MN
PalmettoHPC
Cluster
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How Does It Work Today
KC Wang Clemson University July 17 2013 9
ISP 1Internet
ISP 2Internet
R&Enet
……
DataCenter
CampusNetwork
ResearchNetwork
R&Enet 1
G
Down the road• compliances• User-specific
privileges• access control
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What Are We Building NOW
KC Wang Clemson University July 17 2013 10
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Porting GENI Research Prototype to ProductionSOS: Seamless Large Data Transport
KC Wang Clemson University 11July 17 2013
Perceived point-to-point or multi-point connection
SOS-enabledswitch
SOS-enabledswitch
SOSController
1
2
3.1
4.1
SOSagent
SOSagent
3.2
4.2
SOS pipe
TCP TCP
SOSUW-Madison
SOSClemson
SOSStanford
SOSSCinet
GENIcore
Steroid OpenFlow Service (SOS)by Aaron Rosen and KC Wang
• Seamless TCP throughput upgrade, e.g., 2.5 Mbps 120 Mbps• Multipath support• Automatic site agent detection
Upcoming demos of SOS:
• NSF 12th GENI conference, Kansas City, MO.• Supercomputing 2011, Seattle, WA.
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Condo of Condos:Connecting Campus HPC with SDN
KC Wang Clemson University July 17 2013 12
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Significance of IT Support Team to Bootstrap Researcher Use of HPC and SDN
KC Wang Clemson University
May 2010: Galen joins CITI and begins recruiting & training
users
New Palmetto Cluster Users
Num
ber o
f Use
rs
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And to Create a Transformative University• a unique coalition among academy, IT, and industrial partners
within and beyond Clemson.
• Synergy with other university research centers: Cyberinstitute, ICAR, and Watts Innovation Center
KC Wang Clemson University July 17 2013 14
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Synergy with Cross-Communities Momentum
KC Wang Clemson University July 17 2013 15
Research Communities Companies
Open Source Communities IT Communities
Universities
. . .