Introduction of NISN andBioinformatics applications

Seok Jong Yu, Ph.D.

High-Performance Biocomputing Team / NISN

Contents

• Introduction of KISTI and NISN

• Resource and Services

• Bioinformatics applications

• Conclusion

About KISTIKorea Institute of Science Technology and Information

About KISTI

President

National Nano-Technology Policy Center

Div. of Advanced Information Research

Div. of P

olicy Research

Information S

ervice Center

Softw

are Research C

enter

Technology Information A

nalysis Center

Industry Information A

nalysis Center

SM

B K

nowledge S

upport Center

Div. of P

lanning

Div. of A

dministration

Div. of Information Analysis

NTIS

Center

Supercom

puting Service C

enter

Supercom

puting R&

D C

enter

KR

EO

NE

T Center

Dept. of S

upercomputing S

trategy

National Institute of Supercomputing and Networking

Employees status

• Total 529 Employees (Jan. 2013)

• 120 million$ budget

Government General Fund: 72% Others: 28%!

Personnel(21%) Research(64%) Others(14%) !

Revenue!

Expenses!

US$86! US$34!

US$20! US$58! US$18!

(unit: million)!

(unit: million)!

Researcher!

79%!

Admin.!Techni-cian!

Others!

12%!

6%!3%!

About NISNNational Institute of Supercomputing and Networking

Organization of NISN

Dept. of S

upercomputing Infrastructure

Operation

Dept of Supercomputing Service Integration

Dept of S

upercomputing U

ser Support

Dept. of Global Science Experim

ent Data Hub

Dept. of S

upercomputing Technology

Developm

ent

Dept. of A

dvanced Application E

nvironment

Developm

ent

High-P

erformance B

iocomputing Team

Advanced Visualization Team

Dept of K

RE

ON

ET S

ervice

Dept of S

cience & Technology S

ecurity

Netw

orking Service D

evelopment Team

Sm

art Education S

ervice Team

Supercomputing Service Center Supercomputing R&D Center KREONET Center

National Institute of Supercomputing and Networking

Dept. of Supercomputing Strategy

Personnel : 200 people

Student & Intern3%

Project Based43% Permanent

55%

Form of Employment

Bachelor23%

Master42%

Doctor36%

Degree Obtaioned

Budget : ~48.2Million USD

Resource and Service

Computing Resource

1988 1993 1997 2001

[KISTI-1] Cray 2S

[KISTI-2+] Cray T3E

2002 2003

2 Flops 115 GFlops 320 GFlops

4.4 TFlops 16 GFlops

2GF 16GF 131GF 5.2 TF 2008 2011

360 TF

36 TFlops

324 TFlops

▣ History of KISTI Supercomputers

[KISTI-2] Cray C90

[KISTI-3] NEC SX-5/6

[KISTI-3] IBM p690

[KISTI-4] SUN Blade 6048

[KISTI-4] IBM p595

2009

Computing Resource

Tachyon(SUN)�

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▣ Hardware Specification : Tachyon

!  Cluster system !  Ranked at 14th in top500 in Nov. 2009

Computing Resource

Gaia(IBM)�

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▣ Hardware Specification : Gaia

!  Cluster of SMPs !  Memory intensive computing system for massive parallel jobs !  Ranked at 393th in top500 in Nov. 2009

Networking Resource

IP Network + Optical Private Network 24*365 Network Monitoring by KREONET-NOC

Performance Enhancement & Sharing Operating Information Security Service by CERT-KREONET

Global Network Service

GLObal RIng Network for Advanced Applications Development

!  GLORIAD is the world’s first 10Gbps global R&D network connecting the

entire world with ring-shaped optical network across 15 countries. (Secure

2.5G backup link)

!  Support the data transfer for international-class R&D collaborative research

Bioinformatics Applications

Bioworks• Bioworks is workflow system based on the client-

server architecture

• client tool provides a module that allows constructing workflows

• Bioworks engine on sever side runs the submitted workflows on HPC resourcesBioworks Client

HPC resources Storage resources

Workflow XML File

Bioworks

Bioworks

• Integrated Result Analysis Browser

• provides plug-in GUI components which allow integrative analysis with visualizing tools

Genomics analysisInput&raw&data&

(.fastq)&

Mapping&to&the&&reference&

Execute&cufflink&

Save&GFF3&file&to&&MongoDB&

Execute&&cuffmerge&

DEG&finding&with&cuffdiff&

Convert&BAM&to&&GFF3&Format&

Convert&GTF&to&&GFF3&format&

Mapped&result&(BAM)&

Transcription&Information&File&(gtf,&binary&files,&annotation&

file)&

Transcription&Result&File&&

(GTF)&

gtf&&&annotation&file&

DEG&Result&(GTF)&

Reference&indexing&db&&

! RNA-seq&analysis&tools&�������������������

!  ������������������ �����������������

! ��� ��� �� ����������MongoDB&

insilicoCell

• Client tool supports designing a biological reaction model

• It can import the BioModel database and SBML file

• It simulate the model using ODE tools and Boolean network analysis

• Simulation engine is implemented and installed on server side.

Design of a novel signal transduction pathway

insilicoCellArchitecture of insilicoCell

insilicoCellExamples of a kinetic modeling

Text Mining Tool (BioKnowledge Viewer)• Constructing biological networks using text-ming tool with Pubmed data.

• User can generate own biological interaction network by using on-demand analysis service in NISN

PUBMEDAbstracts

Sentence selector

Relation extractor Rule Sets

Information elementrecognizer

Results

MetaMap

Gene/Protein tagger ABNER

Data Mining Tool and Service

Whole network navigation

Data Mining Tool and Service

Interactive network navigation

SimFlu

• Simulating variation pattern of influenza virus based on genome data for last 10 years from NCBI GenBank.

• Creating variation matrix based on codon variation of influenza virus

• Predicting a virus genome in the future base on simulation

International Collaboration

• NBCR  :  OPAL  development  and  enhancement  job

• HongKong  Univ.  :    Alzheimer’s  disease  research

• UTM  /  UI  /  USM  :  data  mining  of  signal  transducJon

Collaboration with Domestic group

• KIOM  :  constructs  anJ-­‐inflammaJon  signaling  pathway

• KNIH  :  Text-­‐mining  for  Aging  research

• Korea  Ginseng  Corp:  ConstrucJng  ginseng  related  biological  networks

• Korea  Cancer  Center  :  Microarray  analysis  for  cancer  process  

• Amore  Pacific  Corp.  :  melanogenesis  research

• KAIST  :  ConstrucJng  a  NGS  analysis  pipeline

Conclusion

Activities in NISN

• NISN is established and managing the HPC resource and networking services

• Biocomputing team have been developing cyber-research environment for biologist who can’t use UNIX environment.

• Bioworks, insilicoCell, and simFlu have been developed in NISN and used as cyber-research framework and analysis tools.

• We welcome to collaborate with you for constructing a novel cyber research environment on biology field.

Thank you

for your attention