Typed stochastic semantics for the calculus of looping sequences
نویسندگان
چکیده
The Stochastic Calculus of Looping Sequences is a quantitative term rewrite formalism suitable to describe the evolution of microbiological systems, taking into account the speed of the described activities. In this paper we propose an operational semantics for this calculus that considers the types of the species to derive the stochastic evolution of the system. The presence of positive and negative catalysers can modify these speeds. We claim that types provide an abstraction suitable to represent the interaction between elements without specifying exactly the element positions. Our claim is supported through an example modelling the lactose operon.
منابع مشابه
Stochastic Calculus of Wrapped Compartments
The Calculus of Wrapped Compartments (CWC) is a variant of the Calculus of Looping Sequences (CLS). While keeping the same expressiveness, CWC strongly simplifies the development of automatic tools for the analysis of biological systems. The main simplification consists in the removal of the sequencing operator, thus lightening the formal treatment of the patterns to be matched in a term (whose...
متن کاملExtending the Calculus of Looping Sequences to Model Protein Interaction at the Domain Level
In previous papers we introduced a formalism, called Calculus of Looping Sequences (CLS), for describing biological systems and their evolution. CLS is based on term rewriting. Terms can be constructed by composing symbols of a given alphabet in sequences, which could be closed (looping) and contain other terms. In this paper we extend CLS to represent protein interaction at the domain level. S...
متن کاملThe Calculus of Looping Sequences
We describe the Calculus of Looping Sequences (CLS) which is suitable for modeling microbiological systems and their evolution. We present two extensions, CLS with links (LCLS) and Stochastic CLS. LCLS simplifies the description of protein interaction at a lower level of abstraction, namely at the domain level. Stochastic CLS allows us to describe quantitative aspects of the modeled systems, su...
متن کاملTyped Reductions of CLS
The calculus of looping sequences is a formalism for describing the evolution of biological systems by means of term rewriting rules. We enrich this calculus with a type discipline, derived from the requirement of certain elements and the repellency of others, and a type semantic, based on rules respecting different biological properties.
متن کاملStochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways
The paper presents the Stochastic Calculus of Looping Sequences (SCLS) suitable to describe microbiological systems, such as cellular pathways, and their evolution. Systems are represented by terms. The terms of the calculus are constructed by basic constituent elements and operators of sequencing, looping, containment and parallel composition. The looping operator allows tying up the ends of a...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Theor. Comput. Sci.
دوره 431 شماره
صفحات -
تاریخ انتشار 2012