christian rausch, 23 may 2014 cca drylab current development focus
TRANSCRIPT
ICT
Shell 1
Pre-processing of raw “machine” data
Shell 2
Data interpretation &Data integration
Shell 3
Bioinformatics & Sys. Biol. Research Groups
Drylab … a spherical cake
lekker zeg!
CCA Drylab
ICT
DNA-NGS
Daoud Sie
Proteomics
Thang Pham
Shell 1 Preprocessing of raw “machine” data
Oncology
Oncogenetics
RNA-NGSIrsan Kooi
Shell 2 Data interpretation &Data integration
Focus of Research groups
Oncoproteomics
Functional Genomics
Constitutional
Genomics
Tumor genome analysis
Tumor profiling Cancer
Genomics
Departments
Clinical Genetics
Oto-laryngolo
gyPathology
Hematology
Pediatric Oncology
Bio
stat
istics
Gen
omic
s
VUm
c Shell 3 VU and external: Bioinformatics & Sys. Biol. Research Groups
Functional RNAs
Renee de Menezes
Integration
RNA/DNAWessel v
Wieringen
Mol. Pathology
Chairs Strategic Board
Wim van Criekinge
Bauke YlstraCoordi-nator
ChristianRausch
• Galaxyo “more
bioinformatics power to Shell 2”
o Sustainable development of tools
• www.drylab.nl
• Seminars and hands-on workshops
Genomics Mark vd Wiel
Connie Jimenez
Victor van Beusechem
Bauke Ylstra
Eric Sistermans
Ruud Brakenhoff
Remond Fijneman
Prof. Mark van de Wiel
Renske Steenbergen
Michiel Pegtel
Daphne v. Beek
Henk Verheul
Frits Peters
Elisa Giovannett
i
Jeroen Beliën
Jacqueline Cloos
Daniëlle Heideman
Gerrit Meijer
Danijela Koppers-Lalic
Daphne de Jong
Wim van Criekinge
Josephine Dorsman
Drylab: current focus
DNAseq
RNAseq
DNAseq analysis (genome resequencing) RNAseq analysis
sRNAseq analysis
Image source: omictools.com
Drylab: focus DNAseq methods
DNAseq analysis (genome resequencing)
Falco (Amplico
n Analysis pipeline)
QDNAseqCommon tools (established)
DNAseq tools
RNAseq analysis
IRNA pipeline (by Irsan &
Najim)
Common tools (established)
RNAseq tools
Drylab: focus RNAseq methods
sRNAseq analysis
sRNAbench (Michael
Hackenberg)
Common tools (established)
sRNAseq tools
Drylab: focus sRNAseq methods
• Centralized Services run on Galaxy
• Software sustainability
• Software usability (user-friendliness)• alpha and beta test users
Drylab: focus software 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 hardware infrastructure
• Training and work shops for users– Network and pathway analysis with Cytoscape (fall)– DNAseq– RNAseq
Drylab: focus education in bioinformatics