Simulating Bacterial Transcription and Translation in a Stochastic π Calculus

Abstract

Abstract. Stochastic simulation of genetic networks based on models in the stochastic π-calculus is a promising recent approach. This paper contributes an extensible model of the central mechanisms of gene expression i.e. transcription and translation, at the prototypical instance of bacteria. We reach extensibility through object-oriented abstractions, that are expressible in a stochastic π-calculus with pattern guarded inputs. We illustrate our generic model by simulating the effect of translational bursting in bacterial gene expression.

Constructing and visualizing chemical reaction networks from pi-calculus models

“…spico [KLN07] associates sets of functions to channels. In [Kut06] an encoding from spico to the stochastic π-calculus is presented that only increases the amount of used channel names, thus yielding larger reaction sets. Since our approach is explicitly designed to deal with large reaction sets it is applicable to spico as well.…”

“…Its stochastic version, called the stochastic π-calculus [Pri95], comes with a stochastic semantics in terms of continuous time Markov chains (ctmc) that allows to account for the dynamics of cell-biological processes. The stochastic π-calculus has been applied in several modeling studies, see for example, [Kut06,TK08,CCG + 09, MJM + 09]. However, due to the origin of the π-calculus in the field of concurrency theory, the basic paradigm of the stochastic π-calculus is the one of process communication, whereas cell-biological systems are rather described in terms of chemical reactions and solutions.…”

“…However, due to the origin of the π-calculus in the field of concurrency theory, the basic paradigm of the stochastic π-calculus is the one of process communication, whereas cell-biological systems are rather described in terms of chemical reactions and solutions. Therefore, efforts have been made to find ways of transforming reaction networks into process communication, see e.g., [PRSS01,Kut06].…”

A Stochastic Pi Calculus for Concurrent Objects

“…We illustrate the modeling power of SpiCO by a frequent control mechanism between molecular interactions, as binding of molecules: mutual exclusion [11,12]. Consider overlapping sites allowing for a unique visitor at a time -i.e.…”

“…SpiCO was indeed developed concomitantly with modeling case studies [12,13]. The main insight behind SpiCO is that concurrent objects (as in programming languages) appropriately represent interacting molecules for systems biology.…”