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

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Presentation on theme: "Christian Rausch, 23 May 2014 CCA Drylab current development focus."— Presentation transcript:

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

2 a Drylab is about …

3 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!

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

5 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 Giovannetti Jeroen Beliën Jacqueline Cloos Daniëlle Heideman Gerrit Meijer Danijela Koppers-Lalic Daphne de Jong Wim van Criekinge Josephine Dorsman

6 Drylab: current focus DNAseqRNAseq DNAseq analysis (genome resequencing) RNAseq analysis sRNAseq analysis Image source: omictools.com

7 Drylab: focus DNAseq methods DNAseq analysis (genome resequencing) Falco (Amplicon Analysis pipeline) QDNAseq Common tools (established) DNAseq tools

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

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

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

11 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

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

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


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