Bioinformatics

The Bioinformatics Facility was created in March 2013 to foster the implementation of bioinformatics applications in projects of the Department of Life Sciences and Medicine (DLSM). As bioinformatics becomes more and more important in many areas of Life Sciences Research, the Bioinformatics Facility aims at providing expertise in this field to the researchers of DLSM.

Mission

The missions of this core facility are mainly data analysis and teaching.

Data analysis

Applying up-to-date analysis methods to DLSM projects
Developing specific tools and methods for DLSM projects

The general data science’s workflow used is from Hadley Wickham:

data-science-explore

H. Wickham - R for data science, licence CC

It applies to any projects since the generic involved steps are most of the time similar.

Teaching

a full semester of teaching biostat2 for bachelor students 5 th semester. Includes 30 hours of lectures and 30 hours of practicals.
Helping users to analyse their own data
provide training in R via a 4 days workshop for the Doctoral School

Expertise

Any DLSM member has access to the facility and can ask for advice or help in their projects.

The fields of expertise of the bioinformatic facility include:

Statistics

Hypothesis testing, comparison of n samples with correction for multiple testing
Regression model: linear, generalised linear, mixed, non-linear
Global model or many per atomic elements
Power analysis

Computational biology

Next-Generation Sequencing, mapping, from raw sequence files to alignments
Intensive computation is performed on the ULHPC clusters.

Genomics

Copy Number Variation, variant calling together with Dr. Patrick May, Head of Genome Analysis, LCSB.
Genomic scans for genes underlying selective sweeps
Population splits and demographic inferences

Functional Genomics

ChIP-seq, DNA methylation with Dr. Lasse Sinkkonen, Head of the Epigenetics team
Gene expression, microarray pre-processing and comparative analyses
RNA-seq
Functional enrichments (GSEA, IPA ingenuity)

Phylogeny

Proteomics

Reproducible science

all code is versioned via git hosted at r3 LCSB gitlab
an online lab-book (access restricted within UNI) keeps track of daily actions and summarised statistics
- git commits, code insertions / deletions
- per project, per team and per year
reports as Rmarkdown documents. Those text files are versioned and contain all code and links to import raw data, tidying methods and transformation and plotting.

Data visualisation