TY - GEN
T1 - Temporal logic constraints in the biochemical abstract machine BIOCHAM
AU - Fages, François
PY - 2006/7/10
Y1 - 2006/7/10
N2 - Recent progress in Biology and data-production technologies push research toward a new interdisciplinary field, named Systems Biology, where the challenge is to break the complexity walls for reasoning about large biomolecular interaction systems. Pioneered by Regev, Silverman and Shapiro, the application of process calculi to the description of biological processes has been a source of inspiration for many researchers coming from the programming language community. In this presentation, we give an overview of the Biochemical Abstract Machine (BIOCHAM), in which biochemical systems are modeled using a simple language of reaction rules, and the biological properties of the system, known from experiments, are formalized in temporal logic, In this setting, the biological validation of a model can be done by model-checking, both qualitatively and quantitatively, Moreover, the temporal properties can be turned into specifications for learning modifications or refinements of the model, when incorporating new biological knowledge.
AB - Recent progress in Biology and data-production technologies push research toward a new interdisciplinary field, named Systems Biology, where the challenge is to break the complexity walls for reasoning about large biomolecular interaction systems. Pioneered by Regev, Silverman and Shapiro, the application of process calculi to the description of biological processes has been a source of inspiration for many researchers coming from the programming language community. In this presentation, we give an overview of the Biochemical Abstract Machine (BIOCHAM), in which biochemical systems are modeled using a simple language of reaction rules, and the biological properties of the system, known from experiments, are formalized in temporal logic, In this setting, the biological validation of a model can be done by model-checking, both qualitatively and quantitatively, Moreover, the temporal properties can be turned into specifications for learning modifications or refinements of the model, when incorporating new biological knowledge.
U2 - 10.1007/11680093_1
DO - 10.1007/11680093_1
M3 - Conference contribution
AN - SCOPUS:33745606245
SN - 3540326545
SN - 9783540326540
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 1
EP - 5
BT - Logic Based Program Synthesis and Transformation - 15th International Symposium, LOPSTR 2005, Revised Selected Papers
T2 - 15th International Symposium on Logic Based Program Synthesis and Transformation, LOPSTR 2005
Y2 - 7 September 2005 through 9 September 2005
ER -