Resources

s e r v e r s

ArrayMining

ArrayMining Online microarray data mining tool using ensemble and consensus methods for statistical analysis of the gene expression data.

BacillusRegNet

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

DasBOL

DasBOL Data services for the Synthetic Biology Open Language (SBOL) ecosystem.

EnrichNet

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

PSP server

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

PathExpand

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

ProCKSI

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

SBOL stack

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

TopoGSA

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

Virtual Parts

Virtual Parts A database of programmatically accessible models of biological parts (SVPs) for model-based design in synthetic biology.

pm-cmp

pm-cmp Scalable service for automated comparison of large number of protein models implemented on the Google App Engine cloud platform.

ssapredict

ssapredict A web service selecting the fastest stochastic simulation algorithm (SSA) based on topological properties of a given bio-chemical model.

s o f t w a r e

BioHEL

BioHEL Evolutionary learning system, a successor of GAssist, designed to handle large scale bioinformatics datasets and using CUDA for GPU computing.

BioHEL RPE

BioHEL RPE Rule post-processing engine for rules generated with BioHEL, that tries to reduce the rules complexity and improve their generality.

Entanglement

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

FuNeL

FuNeL A co-prediction approach to generate functional networks derived from the rules of machine learning models.

GAssist

GAssist A Pittsburg learning classifier system (LCS) solving data mining problems using the genetic algorithm to evolve a population of variable-length rule sets.

Infobiotics

Infobiotics Integrated software suite for modelling, simulation, parameter optimisation and model checking of large multi-cellular systems.

JEPETTO

JEPETTO A plugin for Cytoscape performing human gene set enrichment and topological analysis based on interaction networks.

Microbase

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

MoSeC

MoSeC A tool to convert dynamic models of complex genetic circuits into nucleotide sequences ready for synthesising.

RGIFE

RGIFE A feature reduction heuristic for the identification of predictive biomarkers.

SynBAD

SynBAD A CAD framework for the design of synthetic genetic circuits.

VRMLGen

VRMLGen R package to create interactive 3D VRML plots, charts and graphs available directly in a web browser.

VisBOL

VisBOL A visualisation library for synthetic biology designs using the Synthetic Biology Open Language (SBOL) Visual specification.