Christian Rausch

Christian Rausch, 23 May 2014
CCA Drylab
current development focus
a Drylab is about …
Drylab … a spherical cake
lekker
zeg!
ICT
Shell 1
Pre-processing of
raw “machine” data
Shell 2
Data interpretation &
Data integration
Shell 3
Bioinformatics & Sys. Biol.
Research Groups
•
CCA Drylab
Galaxy
o “more bioinformatics
power to Shell 2”
o Sustainable
development of tools
•
•
Integration
RNA/DNA
Wessel v
Wieringen
Genomics
Mark vd
Wiel
www.drylab.nl
Seminars and
hands-on
workshops
Shell 3 VU and external:
Coordinator
Christian
Rausch
Bioinformatics & Sys.
Biol. Research Groups
Shell 2 Data interpretation &
Functional
RNAs
Renee de
Menezes
Data integration
Shell 1 Preprocessing of
raw “machine”
data
Clinical
Genetics
RNA-NGS
Irsan Kooi
Constitution
al Genomics
Hematolog
y
ICT
DNA-NGS
Daoud Sie
Pediatric
Oncology
Pathology
Tumor
profiling
Cancer
Genomics
Mol. Pathology
Department
s
Focus of
Research
groups
Proteomic
s
Thang
Pham
Oncolog
y
Oncogenetic
s
Oncoproteomic
s
Otolaryngolog
y
Functional
Genomics
Tumor genome
analysis
Wim van
Criekinge
Prof. Mark
van de Wiel
Henk Verheul
Daphne v. Beek
Eric
Sistermans
Jeroen
Beliën
Connie Jimenez
Frits Peters
Josephine
Dorsman
Jacqueline
Cloos
Elisa
Victor van
Beusechem Giovannetti
Remond
Fijneman
Michiel Pegtel
Danijela
Koppers-Lalic
Bauke Ylstra
Daniëlle
Heideman
Daphne de Jong
Renske
Steenbergen Gerrit Meijer
Ruud Brakenhoff
Drylab: current focus
DNAseq analysis (genome resequencing)
DNAseq
RNAseq analysis
RNAseq
sRNAseq analysis
Image source: omictools.com
Drylab: focus DNAseq methods
DNAseq analysis (genome resequencing)
Common tools
(established)
DNAseq tools
Falco
(Amplicon
Analysis
pipeline)
QDNAseq
Drylab: focus RNAseq methods
IRNA pipeline (by
Irsan & Najim)
RNAseq analysis
Common tools
(established)
RNAseq tools
Drylab: focus sRNAseq methods
sRNAbench (Michael
Hackenberg)
sRNAseq analysis
Common tools
(established)
sRNAseq tools
Drylab: focus software
infrastructure
• Centralized Services run on Galaxy
• Software sustainability
• Software usability (user-friendliness)
• alpha and beta test users
Drylab: focus hardware
infrastructure
• Usage of virtual machines and separate
Test and Production environments
• Hardware requirements are currently
evaluated
• VUmc private cloud (Green Qloud)
• VUmc Store4ever storage solution
Drylab: focus education in
bioinformatics
• Training and work shops for users
– Network and pathway analysis with Cytoscape (fall)
– DNAseq
– RNAseq
Thanks!
Thanks to all contributors
•
•
•
•
Daoud Sie
Stef van Lieshout
Irsan Kooi
Mariska Bierkens
Thanks for your attention!
Time for your
• Remarks
• Questions