Bioinformatics Core Facility Ernesto Lowy February 2012.

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Presentation transcript:

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 Functions > 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

Next Generation Sequencing data: The challenge > 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! Provides the bioinformatics expertise to analyze the data and the computational infrastructure to manage this data Bioinformatics Unit

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)

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

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.

2012 and beyond… > 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….

2012 and beyond… > 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)

Unit Members Francesco Mancuso Ernesto Lowy Gallego Luca Cozzuto Toni Hermoso Pulido > Wide range of skills and expertise > Happy to answer any specific doubt or request

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 Ernesto Lowy: Phone: You can find us on the 4 th floor (Hospital wing)

THANKS FOR YOUR INTEREST!