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Databases

  • SwissRegulon  •  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. [less]
  • arrayMap  •  arrayMap is a curated reference database and bioinformatics resource targeting copy number profiling data in human cancer. The arrayMap database provides an entry point for meta-analysis and systems level data integration of high-resolution oncogenomic CNA data. [less]
  • MetaNetX  •  MetaNetX.org allows to access, analyse and manipulate genome-scale metabolic networks as well as biochemical pathways. It consistently integrates data from various public resources and makes the data accessible in a standardized format using a common namespace. Models can be interactively compared, analysed (e.g. detection of dead-end metabolites/reactions, flux balance analysis or simulation of reaction/gene knockouts), manipulated and exported. Users can upload their own metabolic models. [less]
  • Progenetix  •  The Progenetix database provides an overview of copy number abnormalities in human cancer from Comparative Genomic Hybridization (CGH) experiments. With >30000 cases from >1000 publications, Progenetix is the largest curated database for whole genome copy number profiles. The current dataset contains >20000 chromosomal CGH and >10000 profiles from genomic array experiments. This data covers hundreds of cancer entities. [less]
  • TCS  •  Database show prediction of interaction specificity in two-component systems. These predictions were made with new Bayesian network method that predicts interaction partners using only multiple alignments of amino-acid sequences of interacting protein domains. [less]

Tools

  • arrayMap  •  arrayMap is a curated reference database and bioinformatics resource targeting copy number profiling data in human cancer. The arrayMap database provides an entry point for meta-analysis and systems level data integration of high-resolution oncogenomic CNA data. [less]
  • Biochemical Pathways  •  Digitized version of the Roche Applied Science "Biochemical Pathways" wall chart. The map, linked to relevant ENZYME database entries, can be browsed online, and keyword searches are available. [less]
  • efmtool  •  The efmtool computes elementary flux modes (EFMs) of metabolic networks. It is implemented in Java and has been integrated into MATLAB (see http://www.mathworks.com). EFM computation is a special case of extreme ray enumeration of polyhedral cones. [less]
  • Genome History  •  A tool to extract duplicate genes and their amino acid and synonymous divergence from completely sequenced genomes.  [less]
  • ISMARA  •  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. [less]
  • MetaNetX  •  MetaNetX.org allows to access, analyse and manipulate genome-scale metabolic networks as well as biochemical pathways. It consistently integrates data from various public resources and makes the data accessible in a standardized format using a common namespace. Models can be interactively compared, analysed (e.g. detection of dead-end metabolites/reactions, flux balance analysis or simulation of reaction/gene knockouts), manipulated and exported. Users can upload their own metabolic models. [less]
  • Phylogibbs  •  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. [less]
  • Progenetix  •  The Progenetix database provides an overview of copy number abnormalities in human cancer from Comparative Genomic Hybridization (CGH) experiments. With >30000 cases from >1000 publications, Progenetix is the largest curated database for whole genome copy number profiles. The current dataset contains >20000 chromosomal CGH and >10000 profiles from genomic array experiments. This data covers hundreds of cancer entities. [less]
  • The Systems Biology Research 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. [less]