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Bioinformatics Core Facility Ernesto Lowy

Bioinformatics Core Facility Ernesto Lowy. February 2012. Overview. > Bioinformatics unit : Primary Functions > Services > Equipment > 2012 and beyond > Unit members > How to contact us. Bioinformatics Unit: Primary F unctions. > Support a wide range of users in their

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Bioinformatics Core Facility Ernesto Lowy

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  1. Bioinformatics Core Facility Ernesto Lowy February 2012

  2. Overview >Bioinformaticsunit: PrimaryFunctions >Services >Equipment > 2012 andbeyond > Unit members > How tocontactus

  3. Bioinformatics Unit: PrimaryFunctions > Support a wide range of users in their Bioinformatics-related tasks Wet-lab scientists with no Bioinformatics background OR Bioinformatics researchers lacking knowledge in a certain field. • > This support consists on: • Bioinformatics/Statistics consultation (Before/After performing the experiment) • Develop custom scientific software • Programs to solve a specific problem for which there are not tools available • -Advanced data analysis • Expertise in the Bioinformatics tools available

  4. NextGenerationSequencing data: Thechallenge > Unprecedented flood of data produced by the High-Throughput technologies Illumina sequencers (Genome Analyzers I/II/IIe/Iix,HiScan and HiSeq) generate several million of reads per run > Data yield of a single lane from a HiSeq instrument is 145 million of reads (Single-End run)! File containing the reads occupy 27 GB! Bioinformatics Unit Provides the bioinformatics expertise to analyze the data and the computational infrastructure to manage this data

  5. Services I • > Data analysis • -Resequencing for polymorphism detection, ChIP-seq, RNA-seq, • De-novo transcriptome/genome assembly… • - Microarrays (Gene expression arrays, Methylation arrays, CGH arrays, • SNP arrays) • - Data visualization (Genomic alignments, Genomic annotations, etc..) • - Proteomics • > Downstream data analysis • -GO,GSEA,Pathway analysis, dna motif analysis (novel and known)

  6. Services II • > Scientific programming • - Database/Web programming • - Database maintenance • - Development of Lab data management systems based on Wikipedia technology • -Custom script development for data processing and analysis • > Training • - Bioinformatics tools and analyses • - Programming languages

  7. Equipment > The unit has state-of-the-art scientific computing facilities that allow us to accomplish heavy computing tasks > Linux cluster of ~500 cores with nodes ranging from 48 to 512 GB of memory > 2 Data Storage systems of 260 TB and 700 TB respectively > Web cluster with 112 cores and 48GB per node for web services > Dedicated servers to host public and user databases.

  8. 2012 andbeyond… > Improve our existing pipelines (standardized workflows) > Implement pipelines for other demanded data analysis > Prepare for the arrival of the new technologies Third-generation sequencing, single-cell analysis etc… > Improve the general PRBB bioinformatics skills: TRAINING > And much more….

  9. 2012 andbeyond… >In 2012 we will implement a local instance of Galaxy Web-based platform to perform complex bioinformatics analyses for users without programming experience > Containing the most common bioinformatics tools and workflows (including the ones developed at the PRBB)

  10. Unit Members Francesco Mancuso francesco.mancuso@crg.eu Ernesto Lowy Gallego ernesto.lowy@crg.eu Luca Cozzuto luca.cozzuto@crg.eu Toni HermosoPulido toni.hermoso@crg.cat > Wide range of skills and expertise > Happy to answer any specific doubt or request

  11. How tocontactus -The unit is open to all researchers at the PRBB and also to external users anywhere in the world -Please contact Ernesto Lowy: Email: ernesto.lowy@crg.eu Phone: +34933160181 You can find us on the 4th floor (Hospital wing)

  12. THANKS FOR YOUR INTEREST!

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