2. The consequences of the
life science omics revolution
Huge & many data sets
Increased complexity
It has to be on
one of these
+
tapes
=
Overload
3. Dutch Computing
Infrastructure
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
4. e-Science
Computationally
intensive science in
networked
e-BioGrid: e-science approach environment
Problem-Solving
Bridge between BiG Grid and life science community Environments
Software components
Create e-science infrastructure and methods solving ICT obstacles
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)
5. e-BioGrid organization
The life science part of BiG Grid
UvA LU SARA
Timo Breit Joost Kok Maurice Bouwhuis
Selected e-bioscience application areas Irene Nooren Erwin Bakker Machiel Jansen
1. NGS: Next-generation sequencing Han Rauwerda
2. MAT: Microarray technology
3. MAS: Mass spectrometry
4. NSC: Nanoscopy & imaging
5. BBC: Biobanking/Cohort Studies
6. NMR: NMR Spectroscopy & modelling
6. Alignment with NBIC BioAssist
Life Science Research
Task force Tools TA project PSEs
Analysis, design & implementation
Short cooperative projects
compute and storage systems
Installation and running of the
Genomics NGS
Cooperative projects
of software environment
Proteomics MAS
…
Infrastructure
MAT
NCS
Bio-interpret.
Biobanking BBC
Research Support & Operations
Support
BioAssist Engineering Team e-Core Development Team Team
BioAssist e-BioGrid BiG Grid
Bioinformatics e-BioScience ICT Infrastructure
tools oriented oriented
7. 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
8. Get involved
Anyone with relevant
e-BioGrid: status project ideas is invited to
contact us:
info@e-biogrid.nl
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
10. 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
11. 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
12. 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.
13. Also at this conference
Poster 53. Irene Nooren
Application Showcase. Linda Bakker
Workshop. Evert Lammerts
e-BioGrid
Infrastructure support from the e-BioGrid team is
available for life science research
For project proposals contact
Irene Nooren
Project manager e-BioGrid
info@e-biogrid.nl www.e-biogrid.nl
