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?????