Databases

• SwissRegulon • annotations of regulatory sites • [more]
  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]

• MetaNetX • Metabolic Network Repository & Analysis • [more]
  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]
• TCS • interaction specificity in two-component systems • [more]
  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

• Biochemical Pathways • Biochemical Pathways • [more]
  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 • elementary flux modes of metabolic networks • [more]
  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 • duplicate genes from complete genomes • [more]
  Genome History  •  A tool to extract duplicate genes and their amino acid and synonymous divergence from completely sequenced genomes.  [less]
• ISMARA • genome-wide expression data modeling • [more]
  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 • Metabolic Network Repository & Analysis • [more]
  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 • regulatory sites discovery • [more]
  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]
• The Systems Biology Research Tool • software and API for systems biologists • [more]
  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]