1. Clemson NextNet SDN Use Cases for Life Sciences Research Kuang-Ching “KC” Wang Associate Professor Clemson University Sponsored by NSF grant OCI ‐ 1245936 KC Wang Clemson University 1July 17 2013

2. Clemson NextNet: A NSF CC-NIE Project July 17 20132 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 17 20133 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 17 20134 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 17 20135

6. 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 Feltus KC Wang Clemson University July 17 20136

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 163.6 GB (raw) + 31.8 GB (processed) = 195.4 GB of critical data files (<6 hours to process on cluster) Does not include: Intermediate processing files Reference genome (0.72 GB) RAW DATA (uncompressed)PROCESSED DATA (compressed) Slide prepared by Alex Feltus KC Wang Clemson University July 17 20137

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 17 2013 Clemson, SC Vanderbilt, TN Mayo Clinic, MN Palmetto HPC Cluster

9. How Does It Work Today KC Wang Clemson University July 17 20139 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 17 201310

11. Porting GENI Research Prototype to Production SOS: Seamless Large Data Transport KC Wang Clemson University 11July 17 2013 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 17 201312

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 17 201314

15. Synergy with Cross-Communities Momentum KC Wang Clemson University July 17 201315 Research Communities Companies Open Source Communities IT Communities Universities...

16. FURTHER QUESTIONS KWANG@CLEMSON.EDU KWANG@CLEMSON.EDU KC Wang Clemson University July 17 201316