Christian Rausch, 23 May 2014

CCA Drylabcurrent development focus

a Drylab is about …

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

Thanks to all contributors• Daoud Sie• Stef van Lieshout• Irsan Kooi• Mariska Bierkens

Thanks for your attention!

Time for your• Remarks• Questions

Thanks!