TY - GEN
T1 - Some thoughts on the semantics of biocharts
AU - Harel, David
AU - Kugler, Hillel
PY - 2010
Y1 - 2010
N2 - This paper combines three topics to which Amir Pnueli contributed significantly: the semantics of languages for concurrency, the semantics of statecharts, and reactive and hybrid systems. It is also no accident that the main motivation of our paper comes from biological systems: in recent years Amir became interested in these too. In [KLH10] we introduced Biocharts, a fully executable, two-tier compound visual language for modeling complex biological systems. The high-level part of the language is a version of statecharts, which have been shown to be successful in software and systems engineering. These statecharts can then be combined with any appropriately well-defined language (preferably a diagrammatic one) for specifying the low-level dynamics of the biological pathways and networks. The purpose of [KLH10] was to present the main concepts through a biological example and to illustrate the feasibility and usefulness of the approach. Here we discuss some of the questions that arise when one attempts to provide a careful definition of the semantics of Biocharts. We also compare the main requirements needed in a language for modeling biology with the way statecharts are used in software and system engineering.
AB - This paper combines three topics to which Amir Pnueli contributed significantly: the semantics of languages for concurrency, the semantics of statecharts, and reactive and hybrid systems. It is also no accident that the main motivation of our paper comes from biological systems: in recent years Amir became interested in these too. In [KLH10] we introduced Biocharts, a fully executable, two-tier compound visual language for modeling complex biological systems. The high-level part of the language is a version of statecharts, which have been shown to be successful in software and systems engineering. These statecharts can then be combined with any appropriately well-defined language (preferably a diagrammatic one) for specifying the low-level dynamics of the biological pathways and networks. The purpose of [KLH10] was to present the main concepts through a biological example and to illustrate the feasibility and usefulness of the approach. Here we discuss some of the questions that arise when one attempts to provide a careful definition of the semantics of Biocharts. We also compare the main requirements needed in a language for modeling biology with the way statecharts are used in software and system engineering.
UR - http://www.scopus.com/inward/record.url?scp=77955043588&partnerID=8YFLogxK
U2 - 10.1007/978-3-642-13754-9_9
DO - 10.1007/978-3-642-13754-9_9
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AN - SCOPUS:77955043588
SN - 3642137539
SN - 9783642137532
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 185
EP - 194
BT - Time for Verification - Essays in Memory of Amir Pnueli
A2 - Manna, Zohar
A2 - Peled, Doron A.
ER -