Statecharts: A visual formalism for complex systems
Science of Computer Programming
Stochastic simulation of coupled reaction-diffusion processes
Journal of Computational Physics
Computational models of immunological pathways
IPCAT '97 Proceedings of the second international workshop on Information processing in cell and tissues
Communicating and mobile systems: the &pgr;-calculus
Communicating and mobile systems: the &pgr;-calculus
Theoretical Computer Science
Theory of Modeling and Simulation
Theory of Modeling and Simulation
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
COPASI---a COmplex PAthway SImulator
Bioinformatics
Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks
Electronic Notes in Theoretical Computer Science (ENTCS)
A Spatial Extension to the π Calculus
Electronic Notes in Theoretical Computer Science (ENTCS)
Combining micro and macro-modeling in DEVS for computational biology
Proceedings of the 39th conference on Winter simulation: 40 years! The best is yet to come
Component-Based Modelling of RNA Structure Folding
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
Modelling Biological Compartments in Bio-PEPA
Electronic Notes in Theoretical Computer Science (ENTCS)
Multi-resolution spatial simulation for molecular crowding
Proceedings of the 40th Conference on Winter Simulation
Modeling biological reactivity: statecharts vs. Boolean logic
Proceedings of the Working Conference on Advanced Visual Interfaces
A multi-level model accounting for the effects of JAK2-STAT5 signal modulation in erythropoiesis
Computational Biology and Chemistry
Dynamic Compartments in the Imperative Π-Calculus
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Rule-Based Modelling and Model Perturbation
Transactions on Computational Systems Biology XI
Continuous Petri nets: expressive power and decidability issues
ATVA'07 Proceedings of the 5th international conference on Automated technology for verification and analysis
Hierarchical modeling for computational biology
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Some thoughts on the semantics of biocharts
Time for verification
DEVS-based design of spatial simulations of biological systems
Winter Simulation Conference
Compartmental rule-based modeling of biochemical systems
Winter Simulation Conference
A calculus for shapes in time and space
ICTAC'04 Proceedings of the First international conference on Theoretical Aspects of Computing
Beta binders for biological interactions
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
The attributed pi-calculus with priorities
Transactions on Computational Systems Biology XII
A language for biochemical systems: design and formal specification
Transactions on Computational Systems Biology XII
A stochastic semantics for bioambients
PaCT'07 Proceedings of the 9th international conference on Parallel Computing Technologies
Rule-based modelling of cellular signalling
CONCUR'07 Proceedings of the 18th international conference on Concurrency Theory
Adapting rule-based model descriptions for simulating in continuous and hybrid space
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
Osteoporosis: a multiscale modeling viewpoint
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
Trading Computation Time for Synchronization Time in Spatial Distributed Simulation
PADS '11 Proceedings of the 2011 IEEE Workshop on Principles of Advanced and Distributed Simulation
Integrated regulatory networks (IRNs): Spatially organized biochemical modules
Theoretical Computer Science
Multilevel Computational Modeling and Quantitative Analysis of Bone Remodeling
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Rule-based whole body modeling for analyzing multi-compound effects
Proceedings of the ACM sixth international workshop on Data and text mining in biomedical informatics
BioScape: A Modeling and Simulation Language for Bacteria-Materials Interactions
Electronic Notes in Theoretical Computer Science (ENTCS)
Simulating Anti-adhesive and Antibacterial Bifunctional Polymers for Surface Coating using BioScape
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Hi-index | 0.00 |
Most modeling and simulation approaches applied in cell biology assume a homogeneous distribution of particles in space, although experimental studies reveal the importance of space to understand the dynamics of cells. There are already numerous spatial approaches focusing on the simulation of cells. Recently, they have been complemented by a set of spatial modeling languages whose operational semantics are tied partly to existing simulation algorithms. These modeling languages allow an explicit description of spatial phenomena, and facilitate analysis of the temporal spatial dynamics of cells by a clear separation between model, semantics, and simulator. With the supported level of abstraction, each of those offers a different perception of the spatial phenomena under study. In this paper, we give an overview of existing modeling formalisms and discuss some ways of combining approaches to tackle the problem the computational costs induced by spatial dynamics.