btb or not to b(tb) – that’s the question btb grid marianne heling mark de groot michelle...

BTB or not to B(TB) – That’s the question

BTB GRID

Marianne Heling

Mark de Groot

Michelle Niekoop

Bioinformatics – A. van Kampen

Overview

What is GRID? What is E-(bio)science? Introduction Project

Status and future uses Goal Project Collaborators Infrastructure

Advantages/disadvantages

Costs

GRID

GRID:

The Grid is a service for sharing computer power and data storage capacity over the Internet.

GRID

Types: Data GRID Computing GRID Knowledge GRID Information GRID

E-science VS E-bioscience

E-science:Global collaboration in key areas of science and the next generation of infrastructure that will enable it.

E-bioscience: Data handling, preprocessing & fusion Data integration & knowledge representation Process modeling & dynamic simulation Complex systems approach

E-BioScience approach

Analysismethods

ICT infra-structure

Data Analysis & Integrative in-silico

experiments

VL-e

Biologicalknowledge

Model

Biological research domain e-bioscience core domain Enabling science domain

Biologicalphenomena

Biologicalsolutions

Interpretation

Visualization e-BioLab

Dry-Lab

Wet-Lab

Problem-driven

hypothesis

OmicsData

biologicalproblem

Experiment design

Data-driven

hypothesis

Neurosciences

Ecosystemsdynamics

Cellbiology

Dataintegration

& knowledgerepresentation

Processmodeling &

dynamicsimulation

Data handling,

preprocessing & fusion

Complexsystems

approach

Exactsciences

Mathematics Computerscience

Informationtechnology

Biologicalresearchdomain

Generice-Bioscienceresearch &developmentcore

Enablingsciencedomains

Technologydomains

Introduction Project

Brain Tumor Bank (BTB): Physical storage of brain tissue of patients Databases containing all relevant patient data

and lab.results.

Goal: Research about glioblastomas in particular. These purposes do not serve direct patient care

BTB

DIO

DIO (Data Integratie ten behoeve van Onderzoek): connects different databases with each

other

LIMS (Laboratory Information Management System): manage samples, laboratory users,

instruments, standards / protocols and (many) other laboratory functions.

Status and Future Uses

Status: BTB will be implemented in the AMC

2007/2008

Future: Why nation wide?

Storage space Computing power Sharing resources, data and results

1. 2. 3.

14. 15.

10.7.

16.

5.

11.

6.

12.

13.

8. 9.

4.

Collaborators

RESEARCHERSCLINICIANS

DIO - AMC

BTBAMC

LIMSAMC

DIO - AZM

BTBAZM

LIMSAZM

DIO - MZG

BTBMZG

LIMSMZG

Security

Research BrokerInformation Service Replica Catalog

Computing Elements

Storage Media

Resources

Enter GRID using software interface that runs on your computer

After clearing security validation, able to talk to the Resource Broker

Resource Broker will find the best resources

to execute your job

Resource Broker will query the Information Service and Replica

Catalog

Once the appropriate resources have been

located, the job is executed…

Resource Broker sends the results back to you

Groningen:1 Security Server1 Storage Element

Amsterdam:1 Resource Broker1 Replica Catalog1 Computing Element1 Storage Element

Nijmegen:1 Storage Element

Utrecht:1 Security Server1 Storage Element

Maastricht:1 Computing Element1 Storage Element

Rotterdam:1 Information Service1 Storage Element

Infrastructure

Influence Medical Informatics

ICT

/ T

ech

nic

al

Par

t

Advantages/Disadvantages

Advantages Closed Network Scale Size [more data available] Computing Technologies More chance of major breakthroughs

Disadvantages It takes a time to implement [approx. 5 years]

Costs

UK e-science programme: £ 213.000.000 € 322.290.300

Parelsnoer project: € 35.000.000

BTB or not to B(TB)? € 37.500.000

Conclusion It is possible

Security has to be optimal Economical resources are available The technology is available

A nationwide BTB provides Better research More valuable data Perform bench marking Provide information for new research

Conclusion A nationwide BTB provides

More variety among the patient data

References

http://gridcafe.web.cern.ch/gridcafe/ http://

www.minocw.nl/documenten/ocwcourant.pdf

http://www.regering.nl UK e-Science Programme Parelsnoer Project Bioinformatics articles [course

materials]

Questions?????