SI
Sergiu Ivanov
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1
WEBRSIM
A web-based reaction systems simulator
Book chapter
(2018)
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Sergiu Ivanov, Vladimir Rogojin, Sepinoud Azimi, Ion Petre
We introduce WEBRSIM, the first web-based simulator for reaction systems. The simulator has an easy-to-use interface where the input is a reaction system and four functionalities: the computation of the interactive process driven by a given context sequence, the behaviour graph of the reaction system, its conservation dependency graph, and all its conserved sets. WEBRSIM comes with a browser-based friendly interface and offers a fast software to support computational modeling with reaction systems.
...
We introduce WEBRSIM, the first web-based simulator for reaction systems. The simulator has an easy-to-use interface where the input is a reaction system and four functionalities: the computation of the interactive process driven by a given context sequence, the behaviour graph of the reaction system, its conservation dependency graph, and all its conserved sets. WEBRSIM comes with a browser-based friendly interface and offers a fast software to support computational modeling with reaction systems.
Journal article
(2016)
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Sepinoud Azimi, Cristian Gratie, Sergiu Ivanov, Luca Manzoni, Ion Petre, Antonio E. Porreca
Reaction systems are a new mathematical formalism inspired by the living cell and driven by only two basic mechanisms: facilitation and inhibition. As a modeling framework, they differ from the traditional approaches based on ODEs and CTMCs in two fundamental aspects: their qualitative character and the non-permanency of resources. In this article we introduce to reaction systems several notions of central interest in biomodeling: mass conservation, invariants, steady states, stationary processes, elementary fluxes, and periodicity. We prove that the decision problems related to these properties span a number of complexity classes from P to NP- and coNP-complete to PSPACE-complete.
...
Reaction systems are a new mathematical formalism inspired by the living cell and driven by only two basic mechanisms: facilitation and inhibition. As a modeling framework, they differ from the traditional approaches based on ODEs and CTMCs in two fundamental aspects: their qualitative character and the non-permanency of resources. In this article we introduce to reaction systems several notions of central interest in biomodeling: mass conservation, invariants, steady states, stationary processes, elementary fluxes, and periodicity. We prove that the decision problems related to these properties span a number of complexity classes from P to NP- and coNP-complete to PSPACE-complete.
Journal article
(2015)
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Sepinoud Azimi, Cristian Gratie, Sergiu Ivanov, Ion Petre
Reaction systems is a new mathematical formalism inspired by the biological cell, which focuses on an abstract set-based representation of chemical reactions via facilitation and inhibition. In this article we focus on the property of mass conservation for reaction systems. We show that conservation of sets gives rise to a relation between the species, which we capture in the concept of the conservation dependency graph. We then describe an application of this relation to the problem of listing all conserved sets. We further give a sufficient negative polynomial criterion which can be used for proving that a set is not conserved. Finally, we present a simulator of reaction systems, which also includes an implementation of the algorithm for listing the conserved sets of a given reaction system.
...
Reaction systems is a new mathematical formalism inspired by the biological cell, which focuses on an abstract set-based representation of chemical reactions via facilitation and inhibition. In this article we focus on the property of mass conservation for reaction systems. We show that conservation of sets gives rise to a relation between the species, which we capture in the concept of the conservation dependency graph. We then describe an application of this relation to the problem of listing all conserved sets. We further give a sufficient negative polynomial criterion which can be used for proving that a set is not conserved. Finally, we present a simulator of reaction systems, which also includes an implementation of the algorithm for listing the conserved sets of a given reaction system.