e-biogrid_nbic conference 2011 april 20
DESCRIPTION
e-BioGrid support in developing e-science infrastructure for life science research.TRANSCRIPT
e-BioGridEnabling Life Science Research
and Development
Irene Nooren
NBIC Conference 2011
Huge & many data setsIncreased complexity
Overload
The consequences of the life science omics revolution
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It has to be on one of these tapes
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Dutch ComputingInfrastructure
High-performance computing and storage resources,
The Life Science Grid
National supercomputer
National compute cluster, GPU’s
Self service High performance compute Cloud
Hadoop
Petabytes of disk and tape storage.
Tailored support, training and advice
e-BioGrid: e-science approach
Bridge between BiG Grid and life science community
Create e-science infrastructure and methods
Inventory of needs and requirements of end-users
Bring together expertise and disciplines
Design and develop e-science based Problem-Solving Environments
Connect commonly used software tools to BiG Grid facilities
Make infrastructure available to life-science researchers
Funded by BiG Grid, led by partners NBIC, Nikhef and NCF (NWO)
e-Science
Computationally intensive science in
networked environment
Problem-Solving Environments
Software components solving ICT obstacles
Selected e-bioscience application areas1. NGS: Next-generation sequencing 2. MAT: Microarray technology3. MAS: Mass spectrometry4. NSC: Nanoscopy & imaging5. BBC: Biobanking/Cohort Studies6. NMR: NMR Spectroscopy & modelling
UvATimo Breit
Irene NoorenHan Rauwerda
LUJoost Kok
Erwin Bakker
SARAMaurice Bouwhuis
Machiel Jansen
e-BioGrid organizationThe life science part of BiG Grid
Alignment with NBIC BioAssist
e-BioScience
Life Science Research
Research
SupportBioAssist Engineering Team
Genomics
Bio-interpret.
Biobanking
Proteomics
…
Sh
ort
co
op
era
tive
pro
jects
Task force Tools TA project PSEs
NGS
MAS
MAT
NCS
BBC
BiG GridBioAssist
Support &
Development Team
Operations
Team
Co
op
era
tive
pro
jects
Analy
sis
, desig
n &
im
ple
menta
tion
of soft
ware
environm
ent
Infr
astr
uctu
re
Insta
llation a
nd r
unnin
g o
f th
e
com
pute
and s
tora
ge s
yste
ms
e-Core
e-BioGrid
Bioinformatics
tools oriented
ICT Infrastructure
oriented
Projects
Main projects 2-3 years in each of the technology areas
1.0 FTE implementer, 0.5 FTE BiG Grid technical support
All 6 have been assigned
Dedicated projects Max. 3 months
Projects may be proposed
e-BioGrid: status
Start e-BioGrid: 1 September 2010
5 main projects ongoing: MAT, NSC, NGS, BBC, NMR
10 dedicated projects ongoing in several technology areas and generic infrastructure
Ongoing life science computing making use of BiG Grid facilities
Get involved
Anyone with relevant project ideas is invited to
contact us:
www.e-biogrid.nl
Example: MAT main project Goal: Create infrastructure to design probes for multistrain
prokaryotic samples in tiling array.
Solution: Microarray platform application using bioinformatics alignment tools
Result: Webbased ArrayDesigner
See Application Showcase
Linda Bakker
Example: NGS dedicated project Goal: GWA study analysis is computationally intensive. Use
computing hardware and technology more efficiently either by making use of GPUs or by optimizing the algorithms used.
Solution: adapting the computing algorithm by using symbolic algebra
Result: 20-40 times gain in computing time
Main objectives e-BioGrid
Create a national support basis for e-BioScience to both expert
bioinformaticians and expert life scientists.
Exploit BIG Grid infrastructure in the life science R&D.
Create functional Problem Solving Environments (PSEs), e-infrastructure for
the selected technology areas that deal with high demand in computing or
data resources
Connect with the NBIC-BioAssist and BiG Grid programs.
e-BioGrid
Infrastructure support from the e-BioGrid team is available for life science research
For project proposals contactIrene Nooren
Project manager e-BioGrid
Also at this conference
Poster 53. Irene Nooren
Application Showcase. Linda Bakker
Workshop. Evert Lammerts
www.e-biogrid.nl