Bioinformatics Core Facility

1. Bioinformatics Core Facility Guglielmo Roma January 2011

2. Overview • Bioinformatics Unit: What is it? • Unit Members • Equipment • Services • How to contact us

3. Bioinformatics Unit: What is it? • A core facility to provide researchers with: • bioinformatics consultation and training • scientific resources development • ad-hoc expertise in programming and advanced data analysis to their research projects • Our main goal is to bridge the gap between high-throughput data generation and their interpretation

4. I have my data, now what??? Core Facility 1 Bioinformatics Core Core Facility 2 Core Facility 3 Researcher Bridging the Next Generation Gap • High-throughput technologies helps researchers to understand how biological systems work (“what is transcribed in cancer cells”, “where do proteins bind the genome”, “what is methylated in patients”, etc.) • Bioinformatics has become an essential component of daily research in biomedical sciences

5. Unit Members • A team of 6 people working at the interface between service and research • Highly interdisciplinary, with background in Biology, Statistics, Computer Science • Focusing primarily on genomics technologies, including microarrays, genotyping, and next-generation sequencing • Always available and happy to interact with people (and not only computers!)

6. Equipment • Computing infrastructure • Linux cluster of ~500 cores with nodes ranging from 48 to 512 GB of memory • A disk server with 360 TB • Several servers dedicated to different tasks, including a cluster for web services, with 112 cores and 48 GB per node • Dedicated servers for hosting in-house developed and public databases • Tight collaboration with B&G Programme and TIC dept

7. Services (I) • Bioinformatics • Consultation on bioinformatics methods • Bioinformatics software evaluation, implementation, and training • Scientific programming/Database development • Software development, optimization, customization, implementation, and end-user training • Development of databases and web-services • Scripting and pipelines for automated analysis • e.g. sequence-based analysis, genome annotation, NGS • Genome annotation projects • Functional annotation of coding and non-coding genes

8. Services (II) • Biostatistics • Study design and experimental design • Data analysis • Microarrays • Deep-sequencing • Proteomics • Downstream analyses • GO, GSEA, Pathway, DNA Motifs detection (de-novo and known), regulatory gene networks analysis, etc. • Meta-analysis and data integration

9. Services (III) • Training activities and workshops • Programming courses • High-throughput data analysis • Individual training UCSC Genome Browser Robert Kuhn, Associate Director of the genome browser will give a hands-on interactive workshop designed to help new users become familiar with the basic paradigm and navigation of the site. Experienced users will discover some of the less obvious tools. Please ask Magali Bartomeus for details (magali.bartomeus@crg.es) Next Feb 7th Workshop

10. 4th floor, Bioinformatics Area Rooms 439.01,439.03 How to contact us • The Unit is open to all researchers at the PRBB and also to external users anywhere in the world. • Please contact Guglielmo Roma: • email: guglielmo.roma@crg.es • phone: +34933160181 You can find us on the 4th floor

11. Thanks for your attention!