Resources
s e r v e r s
ArrayMining
Online microarray data mining tool using ensemble and consensus methods for statistical analysis of the gene expression data.
BacillusRegNet
A database and a cross-species analysis platform for the transcriptional gene regulatory networks of Bacillus species.
EnrichNet
A server performing enrichment analysis based on protein interaction network to detect associations between gene/protein sets.
PSP server
Collection of web services which address protein structure prediction (PSP) sub-problems using Learning Classifier Systems.
PathExpand
A method for expanding the gene sets from cellular pathways with their interaction partners in protein-protein interaction networks.
ProCKSI
Protein structure comparison server that computes a similarity consensus based on variety of measures and provides tools for structural classification.
SBOL stack
A platform to store information about genetic parts using the Synthetic Biology Open Language (SBOL) format.
TopoGSA
A web-tool to visualize and compare network topological properties of gene or protein sets mapped onto interaction networks.
Virtual Parts
A database of programmatically accessible models of biological parts (SVPs) for model-based design in synthetic biology.
pm-cmp
Scalable service for automated comparison of large number of protein models implemented on the Google App Engine cloud platform.
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
Evolutionary learning system, a successor of GAssist, designed to handle large scale bioinformatics datasets and using CUDA for GPU computing.
BioHEL RPE
Rule post-processing engine for rules generated with BioHEL, that tries to reduce the rules complexity and improve their generality.
Entanglement
A high-performance graph framework designed for large-scale data integration tasks.
FuNeL
A co-prediction approach to generate functional networks derived from the rules of machine learning models.
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
Integrated software suite for modelling, simulation, parameter optimisation and model checking of large multi-cellular systems.
JEPETTO
A plugin for Cytoscape performing human gene set enrichment and topological analysis based on interaction networks.
Microbase
A distributed workflow enactor for data and compute intensive applications.
MoSeC
A tool to convert dynamic models of complex genetic circuits into nucleotide sequences ready for synthesising.
RGIFE
A feature reduction heuristic for the identification of predictive biomarkers.
Simbiotics
A simulation platform for 3D modelling of multicellular bacterial populations.
SynBAD
A CAD framework for the design of synthetic genetic circuits.
VRMLGen
R package to create interactive 3D VRML plots, charts and graphs available directly in a web browser.
VisBOL
A visualisation library for synthetic biology designs using the Synthetic Biology Open Language (SBOL) Visual specification.
d a t a s e t s
BacillOndex
A semantically-enriched knowledge database for Bacillus subtilis integrating many different biological concepts as a network of relationships.
GP challenge
A dataset of energy terms and distances to the native structure of 54 protein models used to evolve the energy function correlated with a model distance.
Microarray
Datasets of microarray samples used for the comparative evaluation of rule-based classification with BioHEL and different cross validation schemes.
PSP benchmark
A family of benchmarks from the protein structure prediction field suitable for testing scalability of data mining methods.
k-DNF Functions
A family of syntetic boolean functions with different dimensions of difficulty for evolutionary learning systems.