Bioinformatics Core Facility Ernesto Lowy

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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 - PowerPoint PPT Presentation

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Bioinformatics Core FacilityErnesto LowyFebruary 2012

Overview> Bioinformatics unit: Primary Functions> Services> Equipment> 2012 and beyond > Unit members> How to contact us2

Bioinformatics Unit: Primary Functions> Support a wide range of users in theirBioinformatics-related tasksWet-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 technologiesIllumina 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 Unit4

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. 8

2012 and beyond> In 2012 we will implement a local instance of GalaxyWeb-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 Mancusofrancesco.mancuso@crg.euErnesto Lowy Gallegoernesto.lowy@crg.euLuca Cozzutoluca.cozzuto@crg.euToni Hermoso> Wide range of skills and expertise> Happy to answer any specific doubt or request10

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:Email: ernesto.lowy@crg.euPhone: +34933160181 You can find us on the 4th floor (Hospital wing)