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Showing 7 records out of 7 total

Categories: systems biology, evolutionary biology - Software type(s): website - tool
A genotype network is a graph in which vertices represent genotypes that have the same phenotype. The Genonets Server is a tool that provides the following features: (i) the construction of genotype networks for categorical and univariate phenotypes from DNA, RNA, amino acid or binary sequences; (ii) analyses of genotype network topology and how it relates to robustness and evolvability, as well as analyses of genotype network topography; (iii) multiple interactive visualizations.
keywords: network
Categories: proteomics, (protein modifications), genomics, (characterisation/annotation), systems biology, transcriptomics - Software type(s): website, GUI - tool
MARA models genome-wide expression data in terms of our genome-wide annotations of regulatory sites. For a given expression data-set it infers the key transcription regulators, their sample-dependent activities, and their genome-wide targets.
Categories: genomics, (sequence alignment, similarity search), systems biology - Software type(s): website, CLI, GUI - tool
Phylogibbs is an algorithm for discovering regulatory sites in a collection of DNA sequences, including multiple alignments of orthologous sequences from related organisms.The algorithm uses a Gibbs sampling strategy, takes the phylogenetic relationships of the input sequences rigorously into account, and assigns realistic posterior probabilities to reported sites using a novel annealing+tracking strategy.
Categories: proteomics, IT infrastructure - Software type(s): website - tool
SPARQL playground aims to help newbies to get started with SPARQL. It provides a user friendly interface with a simple dataset and examples.
keywords: network
Categories: proteomics, (protein interactions) - Software type(s): website - database
STRING is a database of known and predicted protein-protein interactions. The database contains information from numerous sources, including experimental repositories, computational prediction methods and public text collections. STRING is regularly updated and gives a comprehensive view on protein-protein interactions currently available.
keywords: network
Categories: genomics, (characterisation/annotation), systems biology, transcriptomics - Software type(s): website - database
SwissRegulon is a database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a clear and comprehensible graphical form.
Categories: systems biology - Software type(s): CLI, GUI - tool
An easy-to-use open source software package and API for systems biologists. It performs multiple analyses on stoichiometric reaction networks and other biological networks, and can be easily extended via a number of plugins.
keywords: metabolism, network