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Welcome to BIOchemical Models Specification tool!

BIOMS is a web application for creation and manipulation with models of biochemical networks. The emphasis is on mass action kinetics and kinetics of genetic regulatory networks.

The main features of BIOMS are:

  • on-line manipulation with database of models
  • cooperation of mass action kinetics, gene transcription kinetics and user defined functions
  • sharing of models in user groups
  • generation of ODEs
  • SBML export/import

Model Construction

There are several ways of contructing models in this tool: creating a new model, cloning an existing model, importing a model from SBML. Procedure for constructing new models:

  • Click ADD in main menu, section My models
  • Specify the name of your model and whether it will be public for other users. You can also give a textual description of your model and set links to external information.
  • Define species and global quantities of the model. You can set initial conditions and external links as well.
  • Define reactions - first choose a kinetics type (mass action, transcription or one of user defined functions). Then type a chemical equation (formal grammar, examples). Finally set role of reaction parameters and eventually their values.

User function definition

You can define a new kinetic law and use it in your models. To do this, click ADD in main menu, section Functions. User functions are described by MathML lambda formula. Example is available below the "New function" form. First define variables of function (<bvar><ci>variable_name</ci></bvar>) and then Content MathML formula.

Contact

For registration and questions contact Jakub Vrbas.