This document summarizes a presentation given by Michael Sullivan at the 2013 AAMC Information Technology in Academic Medicine Conference. It discusses how Internet2 supports biomedical research through its community and network resources, tools for managing big data challenges, and an innovation platform to enable data-intensive science experiments. Internet2 is working to address the big data challenges of transport, security, and storage/compute through its Science DMZ approach, performance monitoring tools, and file transfer solutions.

1. AAMC
2013
Informa0on
Technology
in
Academic
Medicine
Conference
Vancouver
CA
June
5-­‐7,
2013
Michael
Sullivan,
M.D.
Associate
Director,
Health
Sciences,
Internet2
Internet2
Support
for
Biomedical
Research

2. Overview
Internet2
Research
Support
•
•
•
•
Community
and
Network
Data-­‐intensive
Science
Interna0onal
Collabora0on
Innova0on
PlaLorm
Big
Data
Challenges
• Transport
• Security
• Storage
and
Compute
2
–
6/7/13,
©
2012
Internet2

3. Internet2
Community
220
Universi0es
60
Corpora0ons
70
Government
agencies
38
Regional
and
state
networks
65
Interna0onal
R&E
networks
3
–
6/7/13,
©
2010
Internet2

4. Advanced
100G
Produc0on
and
Research
Network
4
–
6/7/13,
©
2010
Internet2

5. Data
Tsunami
Life
Sciences
Physics
Large
Hadron
Collider
Image by: CERN
"
5
–
6/7/13,
©
2012
Internet2
Magne0c
Resonance
Imager
(MRI)

6. Visualizing
Big
Data
Physics
Life
Sciences
LHC
–
Lead
Ion
Collision
MRI
–
Monkey
Brain
Source: CERN (ALICE detector)
"
Source: Van Wedeen, M.D., Martinos Center and Dept. of Radiology,
Massachusetts General Hospital and Harvard University Medical School
"
6
–
6/7/13,
©
2012
Internet2

7. Sequencing:
Smaller,
Faster,
Cheaper
Illumina HiSeq 2500/1500
Source: http://www.illumina.com/systems/hiseq_systems/hiseq_2500_1500.ilmn
"
7
–
6/7/13,
©
2012
Internet2
Handheld USB Sequencer
"
Image: Oxford Nanopore Technologies
"

8. Democra0za0on
of
Sequencing
2,386
Genome
Sequencers
Worldwide
–
30
May
2013
Source: Map of High-throughput Sequencers"
8
–
6/7/13,
©
2012
Internet2

9. North
American
Genome
Sequencers
998
Sequencers
in
NA
–
30
May
2013
Source: Map of High-throughput Sequencers"
9
–
6/7/13,
©
2012
Internet2

10. Sequencing
in
Vancouver
13
Sequencers
at
the
Genome
Science
Center
Source: Map of High-throughput Sequencers"
10
–
6/7/13,
©
2012
Internet2

11. Canarie
Weathermap
11
–
6/7/13,
©
2012
Internet2

12. US-­‐based
Interna0onal
Exchange
Points
US-­‐based
Exchange
Points
StarLight,
Chicago
IL
MAN
LAN,
New
York
NY
NGIX-­‐East,
College
Park
MD
Atlan0cWave
(distributed)
AMPATH,
Miami
FL
PacificWave-­‐S,
Los
Angeles
CA
PacificWave-­‐N,
Seahle
WA
12
–
6/7/13,
©
2011
Internet2

13. GEANT
Interna0onal
13
–
6/7/13,
©
2011
Internet2

14. APAN
14
–
6/7/13,
©
2012
Internet2
14
–
6/7/13,
©
2011
Internet2

15. Synchronized
Genomic
Repositories:
NCBI,
EBI,
DDBJ
15
–
6/7/13,
©
2012
Internet2

16. US
–
China
10
Gbps
Link
Dr.
Lin
Fang
Fed
Ex:
2
days
Internet
+
FTP:
26
hours
China-­‐US
10G
Link:
30
seconds
Sample.fa
(24GB)
16
–
6/7/13,
©
2012
Internet2
Dr.
Dawei
Lin

17. Innovation Platform
100
GigE
Layer
2
ConnecOon
Science
DMZ
SoWware
Defined
Networking
SDN
Control
Server
Internet2
innovaOon
backbone
delivered
as
100G
L1
High-­‐Performance
Layer
2/3
Switch/Router
TradiOonal
regional
and
commodity
providers
Performance
Node
Switches,
data
stores
for
data-­‐intensive
science
IP
Network
Layer
3
GENI
Experiments
Your
Research
StaOc
Layer
2
Dynamic
Layer
2
GENI
?
For
more
informaOon,
see
fasterdata.es.net
InnovaOon
Services
TradiOonal
Switch
Substrate
TradiOonal
L3
Campus
Border
Security
17
–
6/7/13,
©
2012
Internet2
TR-­‐CPS
TradiOonal
Services
TradiOonal
Campus
Border
Router
Campus
Enterprise
Network
R&E
IP
SoWware
Defined
Networking
Substrate
OpOcal
System
Dark
Fiber
www.internet2.edu

18. Innova0on
PlaLorm
Pilot
Sites
18
–
6/7/13,
©
2012
Internet2

19. Mee0ng
the
Big
Data
Challenges
Transport
•
•
•
•
Science
DMZ
PerfSONAR
Toolkit
MaDDash
Tes0ng
Mesh
File
Transfer
Tools
Security
• Science
DMZ
Hardening
• Federated
IdM:
InCommon
and
NSTIC
Storage
and
Compute
• Storage
and
Compute
19
–
6/7/13,
©
2012
Internet2

20. Challenge
#1:
Transport
Science
DMZ
hhp://fasterdata.es.net/science-­‐dmz/science-­‐dmz-­‐security/
20
–
6/7/13,
©
2012
Internet2

21. Performance
Monitoring
21
–
6/7/13,
©
2012
Internet2

22. MaDDash
XSEDE
Tes0ng
Mesh
22
–
6/7/13,
©
2012
Internet2

23. File
Transfer
Tools
Unix
LAN
Tools
TCP
–
based
Open
Source
• scp,
smp,
rsync
–
poor
choices
for
WAN
(RTT
>
25ms)
• scp
with
HPN
patch
–
beher
but
s0ll
has
limita0ons
• Globus
Online
–
hhp://www.globusonline.org
– Uses
GridFTP
with
TCP
op0miza0ons
– Friendly
GUI,
Fire
and
Forget,
Galaxy
integra0on
UDP
–
based
• Aspera:
hhp://www.asperasom.com/
Commercial
• Annai
Systems:
hhp://www.annaisystems.com
23
–
6/7/13,
©
2012
Internet2

24. Tool
Speeds
Berkeley,
CA
çè
Argonne,
IL
RTT=53
24
–
6/7/13,
©
2012
Internet2

25. Challenge
#2:
Security
Hardening
the
Science
DMZ
•
•
•
•
ESnet
Big
Data
design
pahern
Internet2
Innova0on
PlaLorm
NSF
CC-­‐NIE
grants
University
of
Florida
–
–
–
–
HIPAA
alignment
Efficient
encryp0on
Comprehensive
logging
Robust
authen0ca0on
25
–
6/7/13,
©
2012
Internet2
Source:
www.securearc.com

26. Federated
Iden0ty
Management
450
Number of Participants
400
350
300
250
200
150
100
50
0
2004
26
–
6/7/13,
©
2012
Internet2
2005
2006
2007
2008
2009
2010
2011 2012 (June)

27. NSTIC
–
Na0onal
Strategy
for
Trusted
Iden00es
in
Cyberspace
•
•
•
•
White
House
iniOaOve
administered
by
NIST
Goal
is
to
create
an
“IdenOty
Ecosystem”
IDEGS
–
IdenOty
Ecosystem
Steering
Group
Five
awards
for
pilots
spanning
mulOple
sectors:
–
–
–
–
–
Resilient
Network
Systems,
AMA,
Aetna,
ACC,
NeHC,
…
Criterion
Systems,
ID/DataWeb,
AOL,
Experian,
Ping
Iden0ty,
…
Daon,
Inc.,
AARP,
PayPal,
Purdue,
…
American
Assoc.
of
Motor
Vehile
Admins,
Microsom,
AT&A,
etc…
Internet2,
Carnegie
Mellon,
Brown,
MIT,
U.
of
Texas,
U.
of
Utah…
27
–
6/7/13,
©
2012
Internet2

28. Challenge
#3:
Storage
and
Compute
• Cloud
CompuOng
–
many
iniOaOves
–
–
–
–
Private:
NCI
bake-­‐off
to
create
Cancer
Knowledge
Clouds
Public/Private:
AWS
EC2
instances
––
[100G]
––
NCBI
repository
Open
Cloud:
BioNimbus
Protected
Data
Cloud
Proprietary:
BGI
EasyGenomics
Cloud
• NaOonal
Cyberinfrastructure
– XSEDE
– Internet2
– NCGAS
28
–
6/7/13,
©
2012
Internet2

29. NCI:
Cancer
Knowledge
Cloud
-­‐
RFI
Summary
of
Community
Input
hhps://wiki.nci.nih.gov/display/NCIPinput/Summary+of+Input+Request%3A+Computa0onal+Needs+to+Support+Large-­‐Scale+Genomics+Inves0ga0ons
29
–
6/7/13,
©
2012
Internet2

30. NCBI:
Four
Different
Approaches
Reduced
Data
Size
Incrementally
Transfer
Large
Files
High
Speed
Network
Connec0ons
Cloud
Access
and
Support
Source:
Don
Preuss,
NCBI
Experiences
and
Big
Data
Strategy,
presented
at
2013
Internet2
Annual
Mee0ng,
Arlington,
VA
30
–
©
2013
Internet2

31. BioNimbus:
An
Open
Cloud
with
Protected
Data
bionimbus.opensciencedatacloud.org

32. EasyGenomics:
BGI’s
Cloud
Solu0on
Source:
Xu
Xing,
Managing
Big
Data:
The
Genome
Center
PerspecBve,
presented
at
Bio-­‐IT
World
Conference
&
Expo
‘13,
Boston,
MA
32
–
6/7/13,
©
2012
Internet2

33. Na0onal
Cyberinfrastructure
• XSEDE
– NSF-­‐funded
– Supercomputers
– HPC
resources
• Internet2
– 220
universi0es
– XSEDEnet
• NCGAS
–
–
–
–
Indiana
University
TACC
SDSC
PSC
33
–
6/7/13,
©
2012
Internet2
Source:
hhps://www.xsede.org/networking

34. NCGAS Virtual Instrument
Indiana
University
6
PB
Storage
NSF-­‐Funded
or
XSEDE
Alloca0on
NCGAS
Galaxy
Portal
5.5
PB
Storage
SDSC
Mason
5
PB
D.C.
POD
Galaxy
Portal
TACC
100
Gig
Internet2
POD
4
PB
Storage
Federally
Funded
10
Gig
NLR
Sequencing
Center
Source:
Barneh,
W.K.,
and
R.D.
LeDuc,
Next
GeneraBon
Cyberinfrastructures
for
Next
GeneraBon
Sequencing
and
Genome
Science,
presented
at
2013
AAMC
GIR
Conference,
Vancouver,
BC
NCBI
PSC

35. Networking
Issues
for
Life
Sciences
Research
Focused
Technical
Workshop
on
July
17-­‐
18,
2013
Lawrence
Berkeley
NaOonal
Laboratory
Berkeley,
California
• Building
on
the
success
of
Joint
Techs,
mee0ng
will
bring
together
technical
experts
in
a
smaller
seyng
with
domain
scien0sts.
• Workshop
will
include
a
slate
of
invited
speakers
and
panels.
• Format
to
encourage
lively,
interac0ve
discussions
with
the
goal
of
developing
a
set
of
tangible
next
steps
for
suppor0ng
this
data-­‐intensive
science
community
• Four
sub-­‐topic
areas:
Network
Architectures,
Workflow
Engines,
Public
and
Private
Cloud
Architectures,
and
Data
Movement
Tools
• See:
hhp://events.internet2.edu/2013/mw-­‐life-­‐sciences/index.cfm
35
–
6/7/13,
©
2012
Internet2

36. Resources
• The
Fourth
Paradigm
–
Data-­‐Intensive
Scien0fic
Discovery
– http://research.microsoft.com/en-us/collaboration/fourthparadigm/
• Internet2
Network
and
Innova0on
PlaLorm
– http://www.internet2.edu/network/
• Science
DMZ
– http://fasterdata.es.net/science-dmz/
• perfSONAR
– http://www.perfsonar.net/
Contact
• Internet2
Research
Support
Center
– rs@internet2.edu
• Internet2
Life
Sciences
–
Michael
Sullivan,
MD,
Associate
Director
– msullivan@internet2.edu
36
–
6/7/13,
©
2012
Internet2

37. Thank
You
INTERNET2
SUPPORT
FOR
BIOMEDICAL
RESEARCH
AAMC
2013
Informa0on
Technology
in
Academic
Medicine
Conference
Vancouver
CA
June
5-­‐7,
2013
Michael
Sullivan,
M.D.
Associate
Director,
Health
Sciences,
Internet2
37
–
6/7/13,
©
2012
Internet2