Centre for Synthetic Biology and the Bioeconomy

Software & Data Repository Resources

Software & Data Repository Resources

We produce a number of software, data repositories and other resources. These are available for the academic scientific community.



Online microarray data mining tool. It uses ensemble and consensus methods for statistical analysis of the gene expression data. Access ArrayMining online.


A semantically-enriched, integrated knowledge base for information about genome annotations, gene regulatory networks, functional interactions, metabolic pathways and microarray experiments. Access BacillOndex online.


A database and a cross-species analysis platform for the transcriptional gene regulatory networks of Bacillus species. Access BacillusRegNet online.


A server performing enrichment analysis. This is based on protein interaction network to detect associations between gene/protein sets. Access EnrichNet online.


A high-performance graph framework designed for large-scale data integration tasks. Access Entanglement online.


A distributed workflow enactor for data and compute intensive applications. Access Microbase online.


A tool to automate the conversion of dynamic models of complex genetic circuits into nucleotide sequences ready for synthesising. Access MoSeC online.


A method for expanding the gene sets from cellular pathways with their interaction partners in protein-protein interaction networks. Access PathExpand online.


Scalable service for automated comparison of large number of protein models. It is implemented on the Google App Engine cloud platform.


Protein structure comparison server. It computes a similarity consensus based on variety of measures. It provides tools for structural classification. Access ProCKSI online.

PSP Server

Collection of web services. These address protein structure prediction (PSP) sub-problems using Learning Classifier Systems.

SBOL Stack

A platform to store information about genetic parts using the Synthetic Biology Open Language (SBOL) format. Access SBOL Stack online.


Standard Virtual Parts (SVPs) is a mapping between genetic parts and their reusable, modular and composable models. Access SVPs online.


A web-tool to visualise and compare network topological properties of gene or protein sets mapped onto interaction networks. Acces TopoGSA online.

Virtual Parts

A database of computationally-accessible models (SVPs) of biological parts. It facilitates model-based design in synthetic biology. Access Virtual Parts online.