On BIOCHAM Symbolic Computation Pipeline for Compiling Mathematical Functions into Biochemistry - Inria - Institut national de recherche en sciences et technologies du numérique
Conference Papers Year : 2024

On BIOCHAM Symbolic Computation Pipeline for Compiling Mathematical Functions into Biochemistry

Abstract

Chemical Reaction Networks (CRNs) are a standard formalism used in chemistry and biology to model complex molecular interaction systems. In the perspective of systems biology, they are a central tool to analyze the high-level functions of the cell in terms of their low-level molecular interactions. In the perspective of synthetic biology, they constitute a target programming language to implement in chemistry new functions either in vitro, in artificial vesicles, or in living cells. In this paper, we describe the CRN synthesis tool part of our CRN modeling and analysis software BIOCHAM (Biochemi- cal Abstract Machine). This compiler transforms any elementary (resp. algebraic) real function into a formal finite CRN to compute it (resp. with absolute functional robustness), through a pipeline of symbolic computation steps, among which quadratization optimization plays a key role to restrict to elementary reactions with at most two reactants and a minimum number of molecular species.
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hal-04602764 , version 1 (05-06-2024)

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  • HAL Id : hal-04602764 , version 1

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François Fages, Mathieu Hemery, Sylvain Soliman. On BIOCHAM Symbolic Computation Pipeline for Compiling Mathematical Functions into Biochemistry. ISSAC 2024 - 49th International Symposium on Symbolic and Algebraic Computation, Jul 2024, Raleigh, NC, United States. ⟨hal-04602764⟩
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