The Biochemical Abstract Machine BIOCHAM

Nathalie Chabrier-Rivier; François Fages; Sylvain Soliman

doi:10.1007/978-3-540-25974-9_14

The Biochemical Abstract Machine BIOCHAM

Nathalie Chabrier-Rivier, François Fages, Sylvain Soliman

INRIA Rocquencourt

Research output: Contribution to journal › Conference article › peer-review

Abstract

In this article we present the Biochemical Abstract Machine BIOCHAM and advocate its use as a formal modeling environment for networks biology. Biocham provides a precise semantics to biomolecular interaction maps. Based on this formal semantics, the Biocham system offers automated reasoning tools for querying the temporal properties of the system under all its possible behaviors. We present the main features of Biocham, provide details on a simple example of the MAPK signaling cascade and prove some results on the equivalence of models w.r.t. their temporal properties.

Original language	English
Pages (from-to)	172-191
Number of pages	20
Journal	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	3082
DOIs	https://doi.org/10.1007/978-3-540-25974-9_14
Publication status	Published - 1 Jan 2005
Externally published	Yes
Event	International Conference on Computational Methods in Systems Biology, CMSB 2004 - Paris, France Duration: 26 May 2004 → 28 May 2004

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10.1007/978-3-540-25974-9_14

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title = "The Biochemical Abstract Machine BIOCHAM",

abstract = "In this article we present the Biochemical Abstract Machine BIOCHAM and advocate its use as a formal modeling environment for networks biology. Biocham provides a precise semantics to biomolecular interaction maps. Based on this formal semantics, the Biocham system offers automated reasoning tools for querying the temporal properties of the system under all its possible behaviors. We present the main features of Biocham, provide details on a simple example of the MAPK signaling cascade and prove some results on the equivalence of models w.r.t. their temporal properties.",

author = "Nathalie Chabrier-Rivier and Fran{\c c}ois Fages and Sylvain Soliman",

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journal = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

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T1 - The Biochemical Abstract Machine BIOCHAM

AU - Chabrier-Rivier, Nathalie

AU - Fages, François

AU - Soliman, Sylvain

PY - 2005/1/1

Y1 - 2005/1/1

N2 - In this article we present the Biochemical Abstract Machine BIOCHAM and advocate its use as a formal modeling environment for networks biology. Biocham provides a precise semantics to biomolecular interaction maps. Based on this formal semantics, the Biocham system offers automated reasoning tools for querying the temporal properties of the system under all its possible behaviors. We present the main features of Biocham, provide details on a simple example of the MAPK signaling cascade and prove some results on the equivalence of models w.r.t. their temporal properties.

AB - In this article we present the Biochemical Abstract Machine BIOCHAM and advocate its use as a formal modeling environment for networks biology. Biocham provides a precise semantics to biomolecular interaction maps. Based on this formal semantics, the Biocham system offers automated reasoning tools for querying the temporal properties of the system under all its possible behaviors. We present the main features of Biocham, provide details on a simple example of the MAPK signaling cascade and prove some results on the equivalence of models w.r.t. their temporal properties.

U2 - 10.1007/978-3-540-25974-9_14

DO - 10.1007/978-3-540-25974-9_14

M3 - Conference article

AN - SCOPUS:26444590537

SN - 0302-9743

VL - 3082

SP - 172

EP - 191

JO - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

JF - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

T2 - International Conference on Computational Methods in Systems Biology, CMSB 2004

Y2 - 26 May 2004 through 28 May 2004

ER -

The Biochemical Abstract Machine BIOCHAM

Abstract

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