Bioinformatics Core Facility Ernesto Lowy
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Bioinformatics Core Facility Ernesto Lowy February 2012
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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
Transcript of Bioinformatics Core Facility Ernesto Lowy
Bioinformatics Core FacilityErnesto 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 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 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 [email protected]
Ernesto Lowy [email protected]
Luca [email protected]
Toni Hermoso [email protected]
> 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:Email: [email protected]: +34933160181
You can find us on the 4th floor (Hospital wing)
THANKS FOR YOUR INTEREST!
