Summary

The EPFL Bioinformatics and Biostatistics Core Facility (BBCF) supports research in life sciences by providing data analysis for large-scale and complex-design genomics experiments, by developping original software and methods, and by providing state-of-the art bioinformatics applications and genomic data through web portals.
 

Introduction

The BBCF is collaborating with life-science researchers and technological facilities to implement a high-quality data analysis and data management infrastructure while offering tailored analyses for complex data. The current focus of the group is on high-throughput sequencing with emphasis on applications to whole-genome sequencing for comparative genomics, ChIP-seq and RNA-seq for functional genomics. Another strong interest of the group is the statistical analysis of dense time-series from live-cell imaging, microarrays or sequencing.

 

Projects and Services

The activities of the BBCF focus on

• Data analysis and statistical consulting

• Software and databases development

• Design and implementation of data management solution

• Bioinformatics training for life science researchers
   

Examples of these include:

Analysis of high-throughput sequencing data

A complete, versatile and configurable pipeline for the analysis of sequencing data combining home-made and selected third-party software is being implemented and parallelized on the Vital-IT cluster. Locally developed solutions include a package for performing an alternative base calling of Illumina data from the fluorescence intensities, and a collection of methods and software for the analysis of ChIP-seq data.

Comparative genome browser

The BBCF has implemented a comparative microbial genome browser that provides a unified access to genomic annotations of all microbial genomes and their syntenic relationships. This consistently integrates information from many external sources, in particular multiple gene predictions and OMA orthology relations through an Ensembl-based web interface.

Multi-omics data management

The BBCF aims to implement a versatile system to manage complete experiments including data produced by a variety of different technologies and to provide browsers and query systems to facilitate the interpretation of these data. Currently the system combines the MIMAS database for microarray and sequencing data, a DAS server and an Ensembl-based genome browser with its Biomart query system. A faster genome browser and a more technology agnostic database is developed to improve the coherence and extensibility of this set.

Statistical analysis and modeling

The group is exploring the potential of stochastic models and multivariate statistics to extract meaning from high-throughput genomic data. One example is the analysis of circadian genes from microarray time series where temporal profiles can be classified according to a few dynamical variables. These pre-computed statistics are searchable through a Biomart query system and allow to explore associations between dynamical and functional properties of a set of genes.

Websites for Further Information

Bioinformatics and Biostatistics Core Facility  http://bbcf.epfl.ch/
Genome browser and query system http://bbcfbrowser.epfl.ch
Comparative genome browser http://microbe.vital-it.ch