Bioinformatics & IT

Big data happen. Molecular biology has moved into an era in which experiments generate huge amounts of data that is difficult, if not impossible to make sense of without making use of the analytical power of computers. The application of computational tools and analysis is known as bioinformatics and is an essential thread of modern biology. The bioinformatics team work to provide state-of-the art bioinformatics to support The Sainsbury Laboratory's research programs. Our efforts are focussed in four areas:

  1. Analysis and Data Exploitation
  2. Training
  3. Tool and Resource Development
  4. Systems and Infrastructure Provision

Analysis and Data Exploitation

The primary role of the bioinformatics team is to assist with and consult on the bioinformatic components of the research projects, in this mode we carry out analyses that contribute to studies as fully involved intellectual collaborators. Our particular areas of expertise include genomics in particular assembly and alignment with high-throughput sequencing data, genetic polymorphism detection, homology search and automatic sequence annotation, transcriptomics (microarray and RNA-seq), statistical analysis, mathematical and systems-biology approaches to modelling and visualising data and large scale phosphoproteomics analysis.

A beneficial aspect of being part of The Sainsbury Laboratory is the opportunity to exploit the data generated by the labs in tandem to its primary use and thereby complement the research activities. Previously this has been a fruitful cooperation and has resulted in numerous bioinformatics team led publications based on The Sainsbury Laboratory's work.

Training

Biological insight relies on having the specialist knowledge to interpret experimental data from new technologies and knowledge of the biological systems from which those data were generated. To this end the bioinformatics team carry out an extensive training program to provide bioinformatics skills where necessary. We concentrate on the gamut of skills required by a scientist at The Sainsbury Laboratory, providing training from basic computer use and scripting for the new user up to discussion of new techniques and algorithms in our regular journal clubs and we have planned a series of masterclasses that will exploit and spread the new knowledge being gained by individual scientists as they carry out their research. We maintain a small library of print and digital training resources and a busy calendar of training events much of which may be viewed online here.

Tool and Resource Development

The novel analyses carried out by The Sainsbury Laboratory often require the development and implementation of new tools and databases. We are experienced in Perl, Ruby, Python (and the 'Bio' software libraries for these languages), web-development in HTML/CSS with JavaScript and Flash, R and Bioconductor and relational databases such as MySQL. We have created a wide range of analysis tools and have developed a tool-kit of code libraries to facilitate ad hoc script development. All our tools are free to use for all and can be obtained here.

Systems and Infrastructure Provision

Our tools and analysis pipelines rely on having a sufficiently powerful computing environment that is equally accessible and easy to use. The bioinformatics team work alongside the scientists of The Sainsbury Laboratory and the IT team to provide this environment.

Image Image

 

 

 

 

Information Technology

High Performance Cluster Development and Administration

The Sainsbury Laboratory is currently running a High Performance cluster, these resources are made available to all staff under the guidance of the informatics team. The High Performance environment is based on IBM hardware running Debian GNU Linux and utilising Platform LSF to manage users requests. The cluster environment is maintained and is under constant development to keep pace with scientific developments and demands.

Hosting and resource provision

The many different projects undertaken within the laboratory have differing resource requirements. Within The Sainsbury Laboratory we strive to provide the right tool for the job, from desktops to servers, visualization to workflow design. Much work is undertaken to integrate new systems to keep up with current demands, maintain systems stability, data integrity and minimize impacts of hardware failure.

Desktop Computing and Analytical Hardware Computing Support

  • development and maintenance of computers and IT infrastructure throughout the Laboratory.
  • software installation and training
  • maintenance and set up of audio/visual equipment
  • design, implementation and maintainance of the Sainsbury Laboratory website and intranet site.