---
res:
  bibo_abstract:
  - "When designing genetic circuits, the typical primitives used in major existing
    modelling formalisms are gene interaction graphs, where edges between genes denote
    either an activation or inhibition relation. However, when designing experiments,
    it is important to be precise about the low-level mechanistic details as to how
    each such relation is implemented. The rule-based modelling language Kappa allows
    to unambiguously specify mechanistic details such as DNA binding sites, dimerisation
    of transcription factors, or co-operative interactions. Such a detailed description
    comes with complexity and computationally costly executions. We propose a general
    method for automatically transforming a rule-based program, by eliminating intermediate
    species and adjusting the rate constants accordingly. To the best of our knowledge,
    we show the first automated reduction of rule-based models based on equilibrium
    approximations.\r\nOur algorithm is an adaptation of an existing algorithm, which
    was designed for reducing reaction-based programs; our version of the algorithm
    scans the rule-based Kappa model in search for those interaction patterns known
    to be amenable to equilibrium approximations (e.g. Michaelis-Menten scheme). Additional
    checks are then performed in order to verify if the reduction is meaningful in
    the context of the full model. The reduced model is efficiently obtained by static
    inspection over the rule-set. The tool is tested on a detailed rule-based model
    of a λ-phage switch, which lists 92 rules and 13 agents. The reduced model has
    11 rules and 5 agents, and provides a dramatic reduction in simulation time of
    several orders of magnitude.@eng"
  bibo_authorlist:
  - foaf_Person:
      foaf_givenName: Andreea
      foaf_name: Beica, Andreea
      foaf_surname: Beica
  - foaf_Person:
      foaf_givenName: Calin C
      foaf_name: Guet, Calin C
      foaf_surname: Guet
      foaf_workInfoHomepage: http://www.librecat.org/personId=47F8433E-F248-11E8-B48F-1D18A9856A87
    orcid: 0000-0001-6220-2052
  - foaf_Person:
      foaf_givenName: Tatjana
      foaf_name: Petrov, Tatjana
      foaf_surname: Petrov
      foaf_workInfoHomepage: http://www.librecat.org/personId=3D5811FC-F248-11E8-B48F-1D18A9856A87
    orcid: 0000-0002-9041-0905
  bibo_doi: 10.1007/978-3-319-26916-0_10
  bibo_volume: 9271
  dct_date: 2016^xs_gYear
  dct_language: eng
  dct_publisher: Springer@
  dct_title: Efficient reduction of kappa models by static inspection of the rule-set@
...