web portal service on open bioinformatics grid obigrid l.
Download
Skip this Video
Loading SlideShow in 5 Seconds..
Web Portal Service on Open Bioinformatics Grid (OBIGrid) PowerPoint Presentation
Download Presentation
Web Portal Service on Open Bioinformatics Grid (OBIGrid)

Loading in 2 Seconds...

play fullscreen
1 / 19

Web Portal Service on Open Bioinformatics Grid (OBIGrid) - PowerPoint PPT Presentation


  • 510 Views
  • Uploaded on

Life Science Grid Symposium Web Portal Service on Open Bioinformatics Grid (OBIGrid) Konagaya Akihiko RIKEN GSC Bioinformatics Group Outline OBIGrid and Bioinformatics Applications OBISgd: Scalable Genome Database OBITco: Thermus Thermophilus Cyber Outlet

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'Web Portal Service on Open Bioinformatics Grid (OBIGrid)' - niveditha


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
outline
Outline
  • OBIGrid and Bioinformatics Applications
  • OBISgd: Scalable Genome Database
  • OBITco: Thermus Thermophilus Cyber Outlet
  • OBIYagns: Yet Another Gene Network Simulator
obigrid open bioinformatics grid
OBIGrid (Open Bioinformatics Grid)

PC Cluster

PC Cluster

  • Isolation by VPN+FW
  • Authentication by Globus
  • Connection via Internet

DB search

program

XMLDB

Cell simulation

program

VPN-FW

VPN-FW

Internet

Site-A

Site-C

VPN-FW

VPN-FW

node

with MDM

Current Status (2003 March)

Academic 11・ Company 9・NRI 5CPU203nodes115

Genome

DB mirror

Seq. anal.

program

MD simulation

program

Site-B

Site-D

slide4

OBIEnv: Bioinformatics Environment (Sato)

Resource

Searcher

  • Single Account
  • Script Prog. Env.
  • Parallel BLAST/DB

Job Acceptance

Jobs

Node

Search

Node

Set

Results

Globus

Tool Kit

Globus

Tool Kit

Resource

Manager

Job Dispatcher

Scanning

Environment

Job Execution Workers

Local

Authentification

Portal

Application

My Script

DB

HW

SW

Mapping of

Local user account

To Grid User Account

Or Public User Account

OBIEnv Users

Other local users not permitted to OBIEnv Access

issues in integrated database
Issues in Integrated Database
  • How to deal with huge datasets?

Scalable XML Database Search System

  • How to deal with heterogeneous datasets?

Computational Pipeline and

Gene Annotation Support System

issues in cell simulation
Issues in Cell Simulation
  • How to estimate unknown parameters?

Differential Equation Simulation + Genetic Algorithm

Requires Enormous Computation

  • How to validate simulation models?

Biological Experiments/ Literature Information

Infrastructure for data/model/knowledge sharing

obisgd distributed xml db browser
OBISgd: Distributed XML DB Browser

XMLDB

XMLDB

Distributed Index Search Servers

XMLDBs

index

search

index

search

index

search

index

search

DDBJ-XML

SOAP

Web

portal

Perl

API

JAVA

API

  • Scalability
  • Quick Response
  • High reliability
slide9

DDBJ-XML

DBs

DDBJ-XML

DBs

DDBJ-XML

DBs

Search

index

Search

index

Search

index

Search

index

PostgreSQL

PostgreSQL

PostgreSQL

PostgreSQL

File Server

System Configuration

Parallel

Search Engine

SOAP Server

Web Server

Parameter:AB000100

getXML_DDBJEntry

Apache

DDBJ-XML

SOAP

Tomcat

XSLT

XML

SELECT * FROM bct1_3 where val like 'BCT%'

XSL

Web

Browser

Candidate Entry List

HTML

slide10

OBITco: Thermus T. Cyber Outlet

Biological

Experimental

Data

Integration of All Information Necessary for

Whole Cell Simulation

Experimental

Analysis

Data

Annotation on

Molecular

Function

Annotation by

Researchers

Automatic Annotation

>S53477 PIR2 release 73.00 MAAIRDYKTALDLTKSLPRPDGLSVQELMDSKIRGGLAYNDFLILPGLVD FASSEVSLQTKLTRNITLNIPLVSSPMDTVTESEMATFMALLDGIGFIHH NCTPEDQADMVRRVKNYENGFINNPIVISPTTTVGEAKSMKEKYGFAGFP VTADGKRNAKLVGAITSRDIQFVEDNSLLVQDVMTKNPVTGAQGITLSEG NEILKKIKKGRLLVVDEKGNLVSMLSRTDLMKNQKYPLASKSANTKQLLW GASIGTMDADKERLRLLVKAGLDVVILDSSQGNSIFQLNMIKWIKETFPD LEIIAGNVVTKEQAANLIAAGADGLRIGMGTGSICITQKVMACGRPQGTA VYNVCEFANQFGVPCMADGGVQKHWSYYYQSFGSWFFYCYDGWYVGRYYR ITR

Genome

Sequence

Database

3D structure

database

Protein

Interaction

Database

Literature

Database

slide11

System overview

Access Manager

SSL connection

OBIGrid network

Thermus server

Secure remote annotation by biologists using SSL on Web Browser

slide12

Annotation system

Top page

Menu page

Annotation page

orf prediction
ORF Prediction
  • 4 programs were used to predict ORF regions in contig sequences.
    • handai (original annotation done by Osaka U.)
    • bdgf (BioDictionary Gene Finding, by T.Shibuya, IBM) [1]
    • getorf1 (with standard genetic code) [2]
    • getorf2 (with bacterial genetic code)
      • getorf is ORF finding and extracting program (part of EMBOSS packages)

[1] Shibuya,T., Rigoutsos, I., “Dictionary-driven prokaryotic gene finding”,

NAR. 30: pp.2710-2725, 2002

[2] http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/getorf.html

slide14

OBIYagns: Cell Simulation Environment

EGF receptor

EGF

SOS

PI3K

Grb2

PKC

Shc

Grb2

SOS

PLC

RAS

NF-kappaB

MAPKKKs

STAT3

STAT1

CyclinD1/cdk4/6

MAPKKs

STAT1

Rb

E2F

Rb-p

STAT3

MAPKs

E2F

MAPKs

STAT1

E2F

STAT3

AP-1

Elk-1

DNADNADNADNADNADNA

Signal Transduction

  • ODE Solver for Stiff Problems
  • Unknown Parameter Estimator

Solver

Web

portal

Mathematical

Modeling

Perl

API

JAVA

API

Cell Cycle

system configuration
System Configuration

Web browser

  • Unknown Parameter Estimation by Real-code Genetic Algorithm
  • (Embarrassing) Parallel Execution of ODE solvers

Remote Execution

PC Cluster

Web server

GA

ODE solver

ODE solver

Task Manager

MPI communication

ODE solver

ODE solver

ODE solver

Results of

Parameter

Estimation

ODE solver

Expandable to GAGrid (Ono)

operation
Operation

  • Selection of reaction type;
    • mass-action, Michaelis-Menten
  • Input of kinetic parameters
  • Input of initial concentrations of reactions
  • Input of fitting data
  • Input of fitting expressions
  • Input of GA parameters, and run GA program
  • Display result of parameter estimation
summary
Summary
  • OBIGrid is practical grid computing test bed over the Internet.
  • 20 sites are connected via VPN and
  • 203 cpus/ 115 nodes are available.
  • Some Web Applications are operational
  • and frameworks for web portal sites and
  • computational pipelines are under development.
obigrid contributors

titles omitted

Staff

OBIGrid Contributors

Kyoko Hirukawa(JAIST),Hiroko Furuno,Sonoko Endo, Keiko Satake(GSC)

VPN/Globus net

Hiroyuki Umeda(IBM)

OBIEnv/OBISgd

Kenji Sato, Xavier Defago(JAIST), Shinichi Tsuji, Yasuhiko Nakajima(HNES)

Makoto Taiji, Tetsu Narumi, Noriyuki Futatsugi, Naoki Takada(GSC),

Tomoyuki Yamamoto(JAIST)

OBIMde

OBITco/ OBIYagns

Fumikazu Konishi, Akinobu Fukuzaki, Ryo Umetsu, Noriko Mito, Aki Hasegawa,

Mariko Hatakeyama, Kaori Ide(GSC)

Seiki Kuramitsu, Shigeyuki Yokoyama, Ryoji Masui, Noriko Nakai(Structurome)

Shuhei Kimura(GSC), Takuji Kawasaki(FUJI RIC)

Grid WG of Japan Committee on High-Performance Computing for Bioinformatics

Masahiro Okamoto(Kushu Uni.), Isao Ono(The Uni. Of Tokushima), Takahiro Koita(OSU), Hiroshi Someya(ISM),

Keisuke Tanaka(Titech), Hideki Nakada( AIST, Titech), Tsuneo Nakanishi( Kushu Uni.),

Tomoyuki Hiroyasu(Dosisha Uni.), Akira Fukuda( Kushu Uni.), Satoshi Matsuoka(Titech),

Masayuki Yamamura( Titech), Tetsushi Yada(HGC), Satoshi Miyazaki(DDBJ), Asao Fujiyama(NII),

Morikazu Nakamura(Uni. Of the Ryukyus), Hiroyuki Kurata(KIT)

Grid WG of Initiative for Parallel Bioinformatics

MITSUBISHI RESEARCH INSTITUTE, Inc.

RIKEN Yokohama Institute

RIKEI Corporation

ESCA, Co.

INTEC Web and Genome Informatics

Corporation

CTC LABORATORY SYSTEMS Corporation

NIPPON SHINYAKU Co,. Ltd.

NEC Corporation

FUJI Research Institute

Corpration

FUJITSU Limited

BEST SYSTEMS Inc

NIPPON TELEGRAPH AND TELEPHONE WEST Corporation

NTT DATA Corporation

Cognitive Research Laboratories, Inc.

Hewlett-Packard Japan, Ltd.

National Institute of Advanced Industrial

Science and Technology

SURIGIKEN Co., Ltd.SUMISHO Eelectronics Co., Ltd.

NEC Software Hokuriku, Ltd.

IBM Japan, Ltd.

Leader Akihiko Konagaya (JAIST, Riken)