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Biochemical Space



Rule is reaction with generalised components. Components of a rule, also called entities, may refer to more than one entity of a reaction. This link forms a hierarchy of entities. Therefore the reaction can be seen as a special case of the rule. This approach is so-called rule-based modelling.


Attributes of a rule:

  1. Name - unique identifier of the rule
  2. Equation - expression of the rule *
  3. Modifier - set of entities which are mandatory in order to apply the rule
  4. Classification - short description of general functionality of the rule
  5. Description - detailed characterization of the rule
  6. Annotation - links to databases with appropriate annotations *
  7. Organisms - set of organisms where the rule might occur *
  8. Notes - additional information


* mandatory (cannot be empty)


Moreover, rule detail provides:

  • explicit enumeration of substrates and products,
  • classification of the rule in process hierarchy,
  • schematical visualisation.



Please use the following reference to cite this web site:
M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: A Web-Based Platform for Systems Biology of Cyanobacteria. In: Computational Methods in Systems Biology, CMSB 2016, Vol. 9859 of LNCS, pp. 316-322. Springer, 2016. DOI