An Excursion Through Quantitative Model Refinement

  • Sepinoud Azimi
  • Eugen Czeizler
  • Cristian Gratie
  • Diana Gratie
  • Bogdan Iancu
  • Nebiat Ibssa
  • Ion PetreEmail author
  • Vladimir Rogojin
  • Tolou Shadbahr
  • Fatemeh Shokri
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9504)


There is growing interest in creating large-scale computational models for biological process. One of the challenges in such a project is to fit and validate larger and larger models, a process that requires more high-quality experimental data and more computational effort as the size of the model grows. Quantitative model refinement is a recently proposed model construction technique addressing this challenge. It proposes to create a model in an iterative fashion by adding details to its species, and to fix the numerical setup in a way that guarantees to preserve the fit and validation of the model. In this survey we make an excursion through quantitative model refinement – this includes introducing the concept of quantitative model refinement for reaction-based models, for rule-based models, for Petri nets and for guarded command language models, and to illustrate it on three case studies (the heat shock response, the ErbB signaling pathway, and the self-assembly of intermediate filaments).


Heat Shock Response Heat Shock Factor Atomic Species Kinetic Rate Constant System Biology Markup Language 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This work was partially supported by the Academy of Finland under project 267915. Bogdan Iancu’s current affiliation is at Department of Mathematics and Statistics, University of Turku, Finland.


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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Sepinoud Azimi
    • 1
    • 3
  • Eugen Czeizler
    • 1
    • 3
  • Cristian Gratie
    • 1
    • 3
  • Diana Gratie
    • 1
    • 3
  • Bogdan Iancu
    • 1
    • 3
  • Nebiat Ibssa
    • 2
  • Ion Petre
    • 1
    • 3
    Email author
  • Vladimir Rogojin
    • 1
    • 3
  • Tolou Shadbahr
    • 1
  • Fatemeh Shokri
    • 1
  1. 1.Department of Computer ScienceÅbo Akademi UniversityTurkuFinland
  2. 2.Department of Information TechnologyUniversity of TurkuTurkuFinland
  3. 3.Turku Centre for Computer Science (TUCS)TurkuFinland

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