Information Processing Letters
PathSim visualizer: an Information-Rich Virtual Environment framework for systems biology
Proceedings of the ninth international conference on 3D Web technology
Bio-PEPA: A framework for the modelling and analysis of biological systems
Theoretical Computer Science
A process model of Rho GTP-binding proteins
Theoretical Computer Science
Efficient, correct simulation of biological processes in the stochastic pi-calculus
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
CiE'10 Proceedings of the Programs, proofs, process and 6th international conference on Computability in Europe
Immune system simulation online
Bioinformatics
Rule-based modelling of cellular signalling
CONCUR'07 Proceedings of the 18th international conference on Concurrency Theory
Spatial modeling in cell biology at multiple levels
Proceedings of the Winter Simulation Conference
Simulating Anti-adhesive and Antibacterial Bifunctional Polymers for Surface Coating using BioScape
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
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We design BioScape, a concurrent language for the stochastic simulation of biological and bio-materials processes in a reactive environment in 3D space. BioScape is based on the Stochastic Pi-Calculus, and it is motivated by the need for individual-based, continuous motion, and continuous space simulation in modeling complex bacteria-materials interactions. Our driving example is a bio-triggered drug delivery system for infection-resistant medical implants. Our models in BioScape will help in identifying biological targets and materials strategies to treat biomaterials associated bacterial infections. The novel aspects of BioScape include syntactic primitives to declare the scope in space where species can move, diffusion rate, shape, and reaction distance, and an operational semantics that deals with the specifics of 3D locations, verifying reaction distance, and featuring random movement. We define a translation from BioScape to 3@p and prove its soundness with respect to the operational semantics.