title: Proteus: a web-based, context-specific modelling tool for molecular networks.
abstract: CONCLUSIONS
  Molecular networks are often studied in diverse cellular or experimental contexts, with highly context-specific details. Modelling introduces further choices as to levels of mathematical description. The resulting possibilities are difficult to explore rapidly, hampering the integration of modelling and experiment. We have developed Proteus, a web-based, context-specific tool for building compartmentalized, ordinary differential equation (ODE) models. It is inspired by the idea of a molecular 'toolkit' for Ca(2+) signalling. Toolkits in Proteus are context-independent representations of biological systems as sets of components, which may correspond to mechanisms of differing levels of complexity. Users pick and choose components from a toolkit and, for each component, pick and choose from different mechanisms, each of which describes a different instantiation of the component's mechanism. Proteus combines these choices into a system of ODEs, which may then be downloaded in SBML (Systems Biology Markup Language), Matlab or Fortran format and independently analyzed. Toolkits, components and mechanisms are user-constructible, either de novo or by cannibalizing existing models, including all those in the Biomodels database. A wide variety of context-specific models may thereby be rapidly built, modified and explored.
  
  
  METHODS
  Proteus, implemented in C#, and a prototype toolkit for modelling calcium signalling are freely and universally available at www.modularmodeling.com
  
  
  BACKGROUND
  gnad.florian@gene.com; jeremy@hms.harvard.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Florian
authors.initials: F
authors.lastname: Gnad
authors.forename: Javier
authors.initials: J
authors.lastname: Estrada
authors.forename: Jeremy
authors.initials: J
authors.lastname: Gunawardena
mesh_terms: D000818:Animals; D016208:Databases, Factual; D020407:Internet; D008954:Models, Biological; D015398:Signal Transduction; D012984:Software; D049490:Systems Biology / Q000379:methods*