Synthetic Biology

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.

Microfluidics
We are particularly interested in the automation of the synthetic biology life cycle, and are using microfluidic technology to achieve some of this aim.

Systems Biology

CISBAN
The Centre for  Integrated Systems Biology of Ageing and Nutrition was one of sis systems biology centres established by the BBSRC 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.

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.

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 an Ondex dataset specifically for Bacillus subtilis.  It contains data from a range of  sources, including physical, genetic and gene expression data.

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.

Computational Intelligence

I am particularly interested in the use of computational intelligence techniques, such as evolutionary computing, for the design of synthetic genetic circuits.