AMOUNTAIN is a novel algorithm to identify active modules from multilayer weighted gene co-expression networks based on a convex optimization approach.
Moksiskaan is a generic database that can be used to integrate information about the connections between genes, proteins, pathways, drugs, and other biological entities. Moksiskaan provides various pathway components for Anduril and may be used to extends its capabilities.
VANESA is a software application for the visualization and analysis of biomedical networks in system biology applications to create systems that can answer fundamental questions and moreover, imitate cell behavior.
ClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network and it can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easely extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be fused to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role.
Pubcrawl is an interactive web application that generates normalized medline distances for terms, and then returns a network topology based on the term distances and protein domain interactions.
M-BISON is a software to implement an efficient method for the integration of biological knowledge with microarray gene expression data to enhance identification of differentially expressed genes