EMBnet Norway
George Magklaras PhD RHCE
Biotechnology Center of Oslo &
The Norwegian Center of Molecular Medicine
University of Oslo, Norway
http://www.biotek.uio.no
http://www.ncmm.uio.no
http://www.no.embnet.org
Talleres Internacionales de Bioinformática - UNAM- Enero 2012
Sunday, December 18, 2011
Agenda
Our facility: users, equipment, services and
activities
What is a life science computing service
environment?
Who are the end users of life science
computing and what do they expect?
Talleres Internacionales de Bioinformática - UNAM- Enero 2012
Sunday, December 18, 2011
EMBnet Norway
overview
Established in 1989.
123 users (mainly from Norway, some
international members)
1 member of staff dedicated to provision of
services to bioinformaticians/Life scientists
In total: 128 processing cores, 768 GPU
cores, 424 Gbytes of RAM, 45 TiBs of disk
space
Talleres Internacionales de Bioinformática - UNAM- Enero 2012
Sunday, December 18, 2011
Some of our users/
synergies
Laboratory for Microbial Dynamics (LaMDa)
http://www.mn.uio.no/farmasi/english/research/groups/lamda/index.html
HT Chemical Biology Screening Platform
http://www.biotek.uio.no/english/research/about/infrastructure/chemical-biology-services/
Donaldson Bioinformatics Group
http://bioinformatics.uio.no/wiki/Donaldson_Group
The High Performance Computing Group (VD)
https://wiki.uio.no/usit/suf/vd/hpc/index.php/VD
The Norwegian Proteomics Society
http://norwegian-proteomics-society.uio.no
Talleres Internacionales de Bioinformática - UNAM- Enero 2012
Sunday, December 18, 2011
Services overview
Access (web/programmatic) Biological
Databases (EMBOSS, GCG, MRS, R), NGS
tools (Galaxy)
Training: Courses plus Focus Groups
GPU life science computing
Development environment support (BioPerl/
C/C++, JAVA, svn)
Provision of RDBMS servers (MySQL,
Postgres) and application portal setup
Talleres Internacionales de Bioinformática - UNAM- Enero 2012
Sunday, December 18, 2011
Training
Hands on and formal courses as part of the
UiO Curriculum ( MBV-INF 4410 MBV-INF
9410 MBV-INF 9410A)
Course subjects include:
Biological sequence database access
Sequence analysis and processing
access of datasets using Perl/Python/
Statistical analysis tools (R + bioconductor)
Talleres Internacionales de Bioinformática - UNAM- Enero 2012
Sunday, December 18, 2011
Life science computing
environment
Provides tools to:
store, manipulate and query Biological sequence and medical
databases (MRS, EMBOSS).
store and process HTS data
integrate scientific instrument workflows into storage and
information repositories (Galaxy, Pipeline Pilot)
Host web portals for groups
Safeguards the user data (privacy,availability,
integrity)
Talleres Internacionales de Bioinformática - UNAM- Enero 2012
Sunday, December 18, 2011
Life science computing
environment (2)
Provide consistent interfaces:
web
GUI
command-line
Talleres Internacionales de Bioinformática - UNAM- Enero 2012
Sunday, December 18, 2011
Talleres Internacionales de Bioinformática - UNAM- Enero 2012
Sunday, December 18, 2011
Talleres Internacionales de Bioinformática - UNAM- Enero 2012
Sunday, December 18, 2011
Talleres Internacionales de Bioinformática - UNAM- Enero 2012
Sunday, December 18, 2011
Talleres Internacionales de Bioinformática - UNAM- Enero 2012
Sunday, December 18, 2011
Life science computing
environment (3)
Provides tools to engage bioinformaticians to:
develop code
adapt existing code
APIs (bioPerl/BioPython) , compilers/
interpreters, version control
Allows them to answer questions/help
people/users.
Talleres Internacionales de Bioinformática - UNAM- Enero 2012
Sunday, December 18, 2011
Life science computing
users
medical
researcher
Y
Web/
GUI
Y
proteomics/
structural
biology
Y
Y
N
medium
functional
genomics
Y
Y
N
medium
Bioinformatics
Y
Y
Y
little
user
type
DBs
CLI
+Dev
N
Help
needed
a lot
Talleres Internacionales de Bioinformática - UNAM- Enero 2012
Sunday, December 18, 2011
GPU computing
Massive acceleration of
algorithms in the field
of life sciences (SIMD)
20x - 200x.
Based on the NVIDIA
Tesla and Fermi GPU
architectures
First Fermi GPU service
in Norway for life
sciences.
Talleres Internacionales de Bioinformática - UNAM- Enero 2012
Sunday, December 18, 2011
Questions?
admin@embnet.uio.no
and
http://www.embnet.org/join/ContactRegistration
Talleres Internacionales de Bioinformática - UNAM- Enero 2012
Sunday, December 18, 2011