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The Next Big Thing Collaborations in the Life Sciences. Gordon K Springer University of Missouri Internet2 Spring Member Meeting April 24, 2012. Developing a 100G TestBed for Life Science Collaborations .

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the next big thing collaborations in the life sciences

The Next Big ThingCollaborations in the Life Sciences

Gordon K Springer

University of Missouri

Internet2 Spring Member Meeting

April 24, 2012

developing a 100g testbed for life science collaborations
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
problem set
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
where does the data come from a high volume est pipeline for discovery
Where Does the Data Come From?A High-Volume EST Pipeline For Discovery

High throughput DNA sequencing at MU DNA Core Facility.

Swine female reproductive tissues and embryos are removed at various times of gestation.

Sequence data analyzed at MU on high-speed systems.

Iterate microarray & other experiments to focus on gene discovery.

Gene annotations quickly obtained by access to other data-bases through the MU Internet2 high speed network.

Improved efficiency, quality and profitability is the goal.

Patterns of gene expression analyzed with microarrays to reveal mechanisms that contribute to reproduction efficiency.

slide5

I70

SL

KC

Col

Big Data/Big Science Collaboratory

university of missouri system
University of Missouri System

Grant Writers Professional Development Sessions

um i nter c ampus n etwork with 100g pathway along i70
UM InterCampusNetwork with 100G Pathway along I70

HtSeq

LSC

Internet2

100G

100G

UM Portion of MOREnet

slide9

OpenFlow

And

Other Protocols

CLOUD

CLOUD

H C R U6

H C R U6

H C R U6

H C R U6

H C R U6

H C R U6

H C R U6

H C R U6

IBM

IBM

IBM

IBM

IBM

IBM

IBM

IBM

LOGIN

LOGIN

Multi-Site Sharing

Protocols

CIFS

NFS

HTTP

FTP

SCP

Protocols

CIFS

NFS

HTTP

FTP

SCP

HPC Infiniband Network

HPC Infiniband Network

Mgmt

Mgmt

Management

Central

Administration

Monitoring

File Mgmt

Management

Central

Administration

Monitoring

File Mgmt

HPC Storage

SMP Servers

Linux Cluster

GPGPUs

HPC Storage

Next-Gen

Linux Cluster

GPGPUs

Machine Room GbE Network

Machine Room GbE Network

Availability

Data Migration

Replication

Backup

Availability

Data Migration

Replication

Backup

Visualization & Display

Visualization & Display

Research Data Store

Research Data Store

Campus GbE Network

Campus GbE Network

Lab (Research

& Clinical)

Lab (Research

& Clinical)

Instruments

(Core Service)

Instrument

(Research)

Instruments

(Core Service)

Instrument

(Research)

Instruments

(Medical)

Instruments

(Medical)

Site A

Site B

openflow at the packet level

OpenFlow-enabled

Commercial Switch

Normal

Software

Secure

Channel

Normal

Datapath

Flow

Table

OpenFlowat the packet level

Controller

PC

User

Storage Cloud

Analysis Engines

NetStorage

NetProcessors

Adapted from: The Stanford Clean Slate Program http://cleanslate.stanford.edu

using middleware tools for vo collaboration
Using Middleware Tools for VO Collaboration

Administrative User

WAYF

2

4

3

14

User

Command

5

Identity Provider

Service Provider

5

1

Credentials

Handle

Service

SHIRE

6

Handle

Identity

Directory

Resource

Manager

Reso

urce

6

Attribute

Authority

Handle

7

Handle

SHAR

13

Credentials

8

YES/NO

Attributes

12

9

VO Entitlement Command

Entitlement Client App

Entitlement Server

11

Command

ES DB

10

YES/NO

Entitlement Server

simplified design

uses public key encryption for authenticationand privacy

Simplified Design

Identity Provider

User

1: request by URL or

command

2

3

5

Entitlement Server

Service Provider

4

6

Page or computational results

getting authenticated
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 this

environment.

slide18
UMBC

http://umbc.rnet.missouri.edu

Grant Writers Professional Development Sessions