title: Colored petri net modeling of small interfering RNA-mediated messenger RNA degradation.
abstract: BACKGROUND
  Mathematical modeling of biological systems is an attractive way for studying complex biological systems and their behaviors. Petri Nets, due to their ability to model systems with various levels of qualitative information, have been wildly used in modeling biological systems in which enough qualitative data may not be at disposal. These nets have been used to answer questions regarding the dynamics of different cell behaviors including the translation process. In one stage of the translation process, the RNA sequence may be degraded. In the process of degradation of RNA sequence, small-noncoding RNA molecules known as small interfering RNA (siRNA) match the target RNA sequence. As a result of this matching, the target RNA sequence is destroyed.
  
  
  METHODS
  In this context, the process of matching and destruction is modeled using Colored Petri Nets (CPNs). The model is constructed using CPNs which allow tokens to have a value or type on them. Thus, CPN is a suitable tool to model string structures in which each element of the string has a different type. Using CPNs, long RNA, and siRNA strings are modeled with a finite set of colors. The model is simulated via CPN Tools.
  
  
  RESULTS
  A CPN model of the matching between RNA and siRNA strings is constructed in CPN Tools environment.
  
  
  CONCLUSIONS
  In previous studies, a network of stoichiometric equations was modeled. However, in this particular study, we modeled the mechanism behind the silencing process. Modeling this kind of mechanisms provides us with a tool to examine the effects of different factors such as mutation or drugs on the process.
authors.affiliation: Department of Electrical and Computer Engineering, Isfahan University of Technology, Isfahan, Iran.
authors.forename: Niloofar
authors.initials: N
authors.lastname: Nickaeen
authors.affiliation: Isfahan Kidney Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
authors.forename: Shiva
authors.initials: S
authors.lastname: Moein
authors.affiliation: Department of Electrical and Computer Engineering, Isfahan University of Technology, Isfahan, Iran.
authors.forename: Zarifeh
authors.initials: Z
authors.lastname: Heidary
authors.affiliation: Department of Electrical and Computer Engineering, Isfahan University of Technology, Isfahan, Iran.
authors.forename: Jafar
authors.initials: J
authors.lastname: Ghaisari
keywords: Colored petri nets; RNA degradation; colored petri nets tools; modeling; small interfering RNA