Bioinformatics Team

From BioWiki

Location: University of Cambridge, UK

Name/Title: Bioinformatics Team, Department of Plant Sciences

Links: Genetics and Epigenetics

Group size:
Krys Kelly - team leader/statistician/bioinformatician
Ruth Dunn - bioinformatician
Tom Hardcastle - statistican/bioinformatician
Rishi Nag - software engineer
Kim Rutherford - software engineer
Dan Tomlinson - systems administrator

Environment:
We are based in David Baulcombe's Genetics and Epigenetics Group in the Department of Plant Sciences in the University of Cambridge UK. Krys Kelly joined the Department of Plant Sciences in April 2008 to set up the bioinformatics team and the other members joined in April, August and October of 2008 and January and February of 2009. Currently, we are mainly working to develop statistical methods and software tools for the analysis of next generation sequencing data and analysing small RNA sequence data in close collaboration with members of the Baulcombe group. Our future aims include developing our programme of bioinformatics research and our collaborations with other members of the Plant Sciences Department.

Tools:
We mainly use mySQL, gbrowse, perl and R. We are developing our pipeline for processing and analysing next generation sequencing data. We also use a wide variety of tools developed by other groups. We support the SIROCCO project.
We are about to submit a paper on a method for the analysis of differential expression of the count data generated by next generation sequencing. The R package is available here: baySeq

Pertinent hardware info:
Our integrated Linux/PC environment is shared by the bioinformaticians and biologists in the lab.

Training:
At the moment this is all very informal through working with people day-to-day. However, we aim to provide training in the future.

Bioinformatics support model:
We work closely with members of the Baulcombe lab to design and analyse experiments aimed at understanding gene silencing in plants. We also collaborate with and support other members of the Plants Sciences Department.

Funding model: Departmental funding and grants