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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.

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Presentation on theme: "Clemson NextNet SDN Use Cases for Life Sciences Research Kuang-Ching “KC” Wang Associate Professor Clemson University Sponsored by NSF grant OCI ‐ 1245936."— Presentation transcript:

1 Clemson NextNet SDN Use Cases for Life Sciences Research Kuang-Ching “KC” Wang Associate Professor Clemson University Sponsored by NSF grant OCI ‐ KC Wang Clemson University 1July

2 Clemson NextNet: A NSF CC-NIE Project July KC 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, optimized 10~40G access to resources on campus and other universities Software defined network (SDN)

3 What is the Fuss About SDN? KC Wang Clemson University July Network Researchers: Industry: Traditional network gettinging unmanageable (not about bandwidth)! Traditional Network SDN

4 What Do Our (Life Sciences) Folks Need? KC Wang Clemson University July 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 Palmetto HPC Cluster Data Store N Data Store N …

5 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 Feltus KC Wang Clemson University July

6 Massive amounts of DNA/RNA/Genetic Data in Databases 1.64 Quadrillion base pairs in 5 yrs! Slide prepared by Alex Feltus KC Wang Clemson University July

7 A NGS Biomarker Example Datasets 5.7GSample_Feltus1_L006_R1.cat.fastq 5.7GSample_Feltus1_L006_R2.cat.fastq 5.8GSample_Feltus1_L007_R1.cat.fastq 5.8GSample_Feltus1_L007_R2.cat.fastq 6.7GSample_Feltus2_L006_R1.cat.fastq 6.7GSample_Feltus2_L006_R2.cat.fastq 6.8GSample_Feltus2_L007_R1.cat.fastq 6.8GSample_Feltus2_L007_R2.cat.fastq 6.5GSample_Feltus3_L006_R1.cat.fastq 6.5GSample_Feltus3_L006_R2.cat.fastq 6.6GSample_Feltus3_L007_R1.cat.fastq 6.6GSample_Feltus3_L007_R2.cat.fastq 7.3GSample_Feltus4_L006_R1.cat.fastq 7.3GSample_Feltus4_L006_R2.cat.fastq 7.4GSample_Feltus4_L007_R1.cat.fastq 7.4GSample_Feltus4_L007_R2.cat.fastq 5.6GSample_Feltus5_L006_R1.cat.fastq 5.6GSample_Feltus5_L006_R2.cat.fastq 5.7GSample_Feltus5_L007_R1.cat.fastq 5.7GSample_Feltus5_L007_R2.cat.fastq 8.8GSample_Feltus6_L006_R1.cat.fastq 8.8GSample_Feltus6_L006_R2.cat.fastq 8.9GSample_Feltus6_L007_R1.cat.fastq 8.9GSample_Feltus6_L007_R2.cat.fastq 2.4GSample_Feltus1_L007_R1.MERGED.BAM 2.7GSample_Feltus2_L006_R1.MERGED.BAM 2.7GSample_Feltus2_L007_R1.MERGED.BAM 2.6GSample_Feltus3_L006_R1.MERGED.BAM 2.6GSample_Feltus3_L007_R1.MERGED.BAM 3.0GSample_Feltus4_L006_R1.MERGED.BAM 3.0GSample_Feltus4_L007_R1.MERGED.BAM 2.2GSample_Feltus5_L006_R1.MERGED.BAM 2.9GSample_Feltus6_L006_R1.MERGED.BAM 2.9GSample_Feltus6_L007_R1.MERGED.BAM 6 RNA Samples in Duplicate GB (raw) GB (processed) = GB of critical data files (<6 hours to process on cluster) Does not include: Intermediate processing files Reference genome (0.72 GB) RAW DATA (uncompressed)PROCESSED DATA (compressed) Slide prepared by Alex Feltus KC Wang Clemson University July

8 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 Clemson, SC Vanderbilt, TN Mayo Clinic, MN Palmetto HPC Cluster

9 How Does It Work Today KC Wang Clemson University July ISP 1 Internet ISP 1 Internet ISP 2 Internet ISP 2 Internet R&E net R&E net … … Data Center Data Center Campus Network Campus Network Research Network Research Network R&E net 1 R&E net 1 G Down the road compliances User-specific privileges access control Down the road compliances User-specific privileges access control

10 What Are We Building NOW KC Wang Clemson University July

11 Porting GENI Research Prototype to Production SOS: Seamless Large Data Transport KC Wang Clemson University 11July 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 12 th GENI conference, Kansas City, MO. Supercomputing 2011, Seattle, WA.

12 Condo of Condos: Connecting Campus HPC with SDN KC Wang Clemson University July

13 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 Number of Users

14 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

15 Synergy with Cross-Communities Momentum KC Wang Clemson University July Research Communities Companies Open Source Communities IT Communities Universities...

16 FURTHER QUESTIONS KC Wang Clemson University July


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