Synthetic Biology

The Programmable Rhizosphere
The Programmable Rhizosphere is a project aimed at engineering bacteria and plants to self-organise and interact with other organisms in a predictable and robust fashion, using the rhizospere (area around the plant roots)  as an example system.

As part of this project we are developing synthetic biology parts for Bacillus subtilis and a range of software.

MoSeC
The Model to Sequence Converter is a tool which takes a simulatable model of a genetic circuit, in the form of an SBML or CellML file and converts it into a standard DNA sequence specification, ready for synthesizing.

Automating biological systems design and implementation
We are particularly interested in the automation of the synthetic biology life cycle, and are using microfluidic technology and robotics to achieve this aim.

Systems Biology

CISBAN
The Centre for  Integrated Systems Biology of Ageing and Nutrition was one of six systems biology centres established by the BBSRC and EPSRC in 2006. CISBAN's aim is to advance understanding of the complex mechanisms underpinning the ageing process and of how these are affected by nutrition, through the field of research known as systems biology.

Saint
Saint is a web application which provides a lightweight annotation integration environment for quantitative biological models. The system enables modellers to rapidly mark up models with biological information derived from a range of data sources.

CID
The Cross-species Interactome Discovery Platform is a system for inferring functional interactions in poorly-annotated organisms, using well-annotated model organisms such as Saccharomyces cerevisiae as a reference.

SyMBa
The Systems and Molecular Biology Archive is a comprehensive data storage and tracking warehouse, built upon the Functional Genomics Experiment (FuGE) standard.

Bioinformatics and Data Integration

Ondex
The Ondex data integration platform enables data from diverse biological data sets to be linked, integrated and visualised through graph analysis techniques. Ondex uses a rich and flexible core data structure, which has the ability to bring together information from structured databases and unstructured sources such as biological sequence data and free text. Ondex also allows users to visualise and analyse the integrated data.

BacillOndex
BacillOndex is a knowledgebase specifically for Bacillus subtilis. The dataset has been created by intgerating a number of different data sources using the Ondex platform.  The data includes physical, genetic and gene expression data. BacillOndex also provides a knowledgebase for mining for new parts to facilitate approaches in Bacillus synthetic biology

BacillusRegNet
BacillusRegNet is a reference database and analysis platform for the analsysis and inference of Bacillus transcriptional regulation networks. Regulatory interactions in poorly-annotated Bacillus species are inferred using data about homology with proteins in B. subtilis. BacillusRegNet uses the same technology as CoryneRegNet.

ParseSNP
ParseSNP is a tool for the systems-level analysis of Single Nucleoptide Polymoriphisms. Built upon the Ondex platform, it allows tracking of SNPs from specific genomic regions to the pathway level.

Cloud Computing

AptaMems

Detecting infectious organisms using a concerted approach using genomics, bioinformatics, molecular engineering and nano-enabled bio-MEMS technologies.