The Many Roads to the Simulation of Reaction Systems

Ferretti, Claudio; Leporati, Alberto; Manzoni, Luca; Porreca, Antonio E.

doi:10.3233/fi-2020-1878

Cited by 4 publications

(1 citation statement)

References 19 publications

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“…In contrast, our approach offers a rewriting-based modeling of RSs, leveraging the extensive functionalities of the Maude environment, which provides multiple built-in functions and third-party tools for program analysis. Other implementations of RSs include brsim [21], a Basic Reaction System Simulator written in Haskell and distributed under the terms of GNU GPLv3 license [22] whose online version WEBRSIM makes all the features of brsim available through a friendly web interface [23]; HERESY [24], a GPU-based Highly Efficient REaction SYstem simulator, that exploits the large number of computational units inside GPUs to boost performance [25]; cl-rs [26], an optimised Common Lisp simulator for RSs presented in [27].…”

Section: Related Workmentioning

confidence: 99%

Modeling and Analyzing Reaction Systems in Maude

Ballis,

Brodo,

Falaschi

2024

Electronics

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Reaction Systems (RSs) are a successful computational framework for modeling systems inspired by biochemistry. An RS defines a set of rules (reactions) over a finite set of entities (e.g., molecules, proteins, genes, etc.). A computation in this system is performed by rewriting a finite set of entities (a computation state) using all the enabled reactions in the RS, thereby producing a new set of entities (a new computation state). The number of entities in the reactions and in the computation states can be large, making the analysis of RS behavior difficult without a proper automated support. In this paper, we use the Maude language—a programming language based on rewriting logic—to define a formal executable semantics for RSs, which can be used to precisely simulate the system behavior as well as to perform reachability analysis over the system computation space. Then, by enriching the proposed semantics, we formalize a forward slicer algorithm for RSs that allows us to observe the evolution of the system on both the initial input and a fragment of it (the slicing criterion), thus facilitating the detection of forward causality and influence relations due to the absence/presence of some entities in the slicing criterion. The pursued approach is illustrated by a biological reaction system that models a gene regulation network for controlling the process of differentiation of T helper lymphocytes.

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Section: Related Workmentioning

confidence: 99%

Modeling and Analyzing Reaction Systems in Maude

Ballis,

Brodo,

Falaschi

2024

Electronics

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A framework for monitored dynamic slicing of reaction systems

Brodo,

Bruni,

Falaschi

2024

Nat Comput

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Reaction systems (RSs) are a computational framework inspired by biochemical mechanisms. A RS defines a finite set of reactions over a finite set of entities. Typically each reaction has a local scope, because it is concerned with a small set of entities, but complex models can involve a large number of reactions and entities, and their computation can manifest unforeseen emerging behaviours. When a deviation is detected, like the unexpected production of some entities, it is often difficult to establish its causes, e.g., which entities were directly responsible or if some reaction was misconceived. Slicing is a well-known technique for debugging, which can point out the program lines containing the faulty code. In this paper, we define the first dynamic slicer for RSs and show that it can help to detect the causes of erroneous behaviour and highlight the involved reactions for a closer inspection. To fully automate the debugging process, we propose to distil monitors for starting the slicing whenever a violation from a safety specification is detected. We have integrated our slicer in BioResolve, written in Prolog which provides many useful features for the formal analysis of RSs. We define the slicing algorithm for basic RSs and then enhance it for dealing with quantitative extensions of RSs, where timed processes and linear processes can be represented. Our framework is shown at work on suitable biologically inspired RS models.

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FPGA Implementation of Reaction Systems

Shang,

Verlan,

et al. 2024

Electronics

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Reaction system (RS) belongs to a type of qualitative computing model inspired by biochemical reactions taking place inside biological cells. It concerns more the interactions and causality among reactions rather than concrete concentrations of chemical entities. Many biochemical processes and models can be represented in the form of reaction systems so that complex relations and ultimate products of a variety of reactions can be revealed qualitatively. The reaction system works in parallel mode. Software simulation of this kind of model may suffer from the penalty of inefficient parallelism for the limited performance of CPU/GPU, especially for the simulation of large-scale models. Considering potential applications of reaction systems in disease diagnoses and in drug developments, hardware implementation of reaction systems provides a better way to accelerate computations involved. In this paper, an FPGA implementation method of a reaction system called RSFIM is proposed. Two small-scale models, i.e., the reaction system of intermediate filaments self-assembly and heat shock response, are implemented on FPGA, achieving a computing speed of 2×108 steps per second. For large-scale models, the ErbB reaction system is implemented, obtaining a speedup of 7.649×104 compared with its highest performance GPU simulation so far. The reaction system binary counter, which is a quantitative model, is also implemented by the Boolean explanation of the qualitative character of the reaction system. FPGA implementation of reaction systems opens a novel research line to speed up the simulations of reaction systems and other biological models in the perspective of parallel digital circuits.

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The Many Roads to the Simulation of Reaction Systems

Cited by 4 publications

References 19 publications

Modeling and Analyzing Reaction Systems in Maude

Modeling and Analyzing Reaction Systems in Maude

A framework for monitored dynamic slicing of reaction systems

FPGA Implementation of Reaction Systems

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