Visualization of developmental processes by extrusion in space-time
GI '96 Proceedings of the conference on Graphics interface '96
The topological structures of membrane computing
Fundamenta Informaticae - Membrane computing
Pattern-matching and rewriting rules for group indexed data structures
ACM SIGPLAN Notices
Accretive Rules in Cayley P Systems
WMC-CdeA '02 Revised Papers from the International Workshop on Membrane Computing
Proceedings of the International Workshop on Graph Transformations in Computer Science
Advanced Functional Programming, Second International School-Tutorial Text
Theoretical Computer Science
Declarative definition of group indexed data structures and approximation of their domains
Proceedings of the 3rd ACM SIGPLAN international conference on Principles and practice of declarative programming
A rewriting logic framework for operational semantics of membrane systems
Theoretical Computer Science
A Spatial Extension to the π Calculus
Electronic Notes in Theoretical Computer Science (ENTCS)
Graph-grammars: An algebraic approach
SWAT '73 Proceedings of the 14th Annual Symposium on Switching and Automata Theory (swat 1973)
Spatial Organization of the Chemical Paradigm and the Specification of Autonomic Systems
Software-Intensive Systems and New Computing Paradigms
RTA'03 Proceedings of the 14th international conference on Rewriting techniques and applications
CiE'10 Proceedings of the Programs, proofs, process and 6th international conference on Computability in Europe
Declarative mesh subdivision using topological rewriting in MGS
ICGT'10 Proceedings of the 5th international conference on Graph transformations
Petri net representation of multi-valued logical regulatory graphs
Natural Computing: an international journal
Qualitative petri net modelling of genetic networks
Transactions on Computational Systems Biology VI
Spatial modeling in cell biology at multiple levels
Proceedings of the Winter Simulation Conference
UCNC'12 Proceedings of the 11th international conference on Unconventional Computation and Natural Computation
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In this paper, we aim at modeling and analyzing the regulation processes in multi-cellular biological systems, in particular, tissues. The modeling framework is a generalization of several existing formalisms. In particular, it can be seen as an extension of logical regulatory networks (a la Thomas) with information about cells' physical state and environment, e.g., their spatial relationships. The resulting formalisms, called integrated regulatory networks (IRNs) is equipped with a transition systems semantics that preserves the possibility of an enumerative and exhaustive state space exploration. This paper presents the modeling framework, its semantics, as well as a prototype implementation that allowed preliminary experiments on some applications related to biology.