1. Christian Rausch, 23 May 2014 CCA Drylab current development focus

2. a Drylab is about …

3. Drylab … a spherical cake
lekker zeg!
ICT
Shell 1
Shell 2
Shell 3
Pre-processing of
raw “machine” data
Data interpretation &
Data integration
Bioinformatics & Sys. Biol. Research Groups

4. CCA Drylab Galaxy www.drylab.nl Seminars and hands-on workshops ICT
“more bioinformatics power to Shell 2”
Sustainable development of tools
Seminars and hands-on workshops
CCA Drylab
Chairs Strategic Board
Wim van Criekinge
Bauke Ylstra
Integration
RNA/DNA
Wessel v Wieringen
Biostatistics Genomics
VUmc
Coordi-
nator
Christian
Rausch
Shell 3
VU and external: Bioinformatics & Sys. Biol. Research Groups
Genomics Mark vd Wiel
Functional RNAs
Renee de Menezes
Shell 2
Data interpretation &
Data integration
Shell 1
Preprocessing of
raw “machine” data
Clinical Genetics
RNA-NGS
Irsan Kooi
ICT
Proteomics
Thang Pham
Constitutional Genomics
Oncology
Hematology
Oncogenetics
Oncoproteomics
DNA-NGS
Daoud Sie
Pediatric Oncology
Oto-laryngology
Pathology
Tumor profiling
Functional Genomics
Departments
Cancer Genomics
Tumor genome analysis
Focus of Research groups
Mol. Pathology

5. Wim van Criekinge
Prof. Mark van de Wiel
Daphne v. Beek
Henk Verheul
Jeroen Beliën
Eric Sistermans
Connie Jimenez
Frits Peters
Josephine Dorsman
Jacqueline Cloos
Victor van Beusechem
Elisa Giovannetti
Remond Fijneman
Michiel Pegtel
Danijela Koppers-Lalic
Bauke Ylstra
Ruud Brakenhoff
Renske Steenbergen
Daniëlle Heideman
Daphne de Jong
Gerrit Meijer

6. Drylab: current focus DNAseq RNAseq RNAseq analysis
DNAseq analysis (genome resequencing)
RNAseq analysis
DNAseq
RNAseq
Analysis of Genome Structure
Copy number profiling
Insertions
Deletions
Breakpoints
Translocations
Inversions
sRNAseq analysis
Image source: omictools.com

7. Drylab: focus DNAseq methods
Falco (Amplicon Analysis pipeline)
DNAseq analysis (genome resequencing)
Analysis of Genome Structure
Copy number profiling
Insertions
Deletions
Breakpoints
Translocations
Inversions
Common tools (established)
DNAseq tools
QDNAseq

8. IRNA pipeline (by Irsan & Najim)
Drylab: focus RNAseq methods
IRNA pipeline (by Irsan & Najim)
RNAseq analysis
Common tools (established)
RNAseq tools

9. sRNAbench (Michael Hackenberg)
Drylab: focus sRNAseq methods
sRNAbench (Michael Hackenberg)
sRNAseq analysis
Common tools (established)
sRNAseq tools

10. Drylab: focus software infrastructure
Centralized Services run on Galaxy
Software sustainability
Software usability (user-friendliness)
alpha and beta test users

11. 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

12. Drylab: focus education in bioinformatics
Training and work shops for users
Network and pathway analysis with Cytoscape (fall)
DNAseq
RNAseq

13. Thanks! Thanks to all contributors Thanks for your attention!
Daoud Sie
Stef van Lieshout
Irsan Kooi
Mariska Bierkens
Thanks for your attention!
Time for your
Remarks
Questions