BioScape: A Modeling and Simulation Language for Bacteria-Materials Interactions
BioScape: A Modeling and Simulation Language for Bacteria-Materials Interactions
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BioScape：细菌与材料相互作用的建模和模拟语言
DOI：
10.1016/j.entcs.2013.02.017
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发表时间：
2013
影响因子：
--
通讯作者：
E. Bonelli
中科院分区：
文献类型：
--
作者：
Adriana B. Compagnoni;Vishakha Sharma;Yifei Bao;M. Libera;S. Sukhishvili;P. Bidinger;L. Bioglio;E. Bonelli
我们设计了一种并发语言Bioscape，用于在3D空间中对生物和生物材料过程进行随机模拟。Bioscape是基于随机PI演算的，它的动机是在模拟复杂的细菌-材料相互作用时需要基于个体的、连续的运动和连续的空间模拟。我们举的例子是一种用于抗感染医疗植入物的生物触发药物输送系统。我们在Bioscape中的模型将有助于确定生物目标和材料策略，以治疗与生物材料相关的细菌感染。Bioscape的新颖方面包括声明物种在空间中可以移动的范围、扩散速度、形状和反应距离的语法原语，以及处理3D位置细节、验证反应距离和随机移动的操作语义。我们定义了一种从BIOSCAPP到3π的转换，并从操作语义的角度证明了它的可靠性。
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 3π and prove its soundness with respect to the operational semantics.
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影响因子：
14
作者：
DESAI, NP;HOSSAINY, SFA;HUBBELL, JA
通讯作者：
HUBBELL, JA
影响因子：
14
作者：
Moskowitz, Joshua S.;Blaisse, Michael R.;Samuel, Raymond E.;Hsu, Hu-Ping;Harris, Mitchel B.;Martin, Scott D.;Lee, Jean C.;Spector, Myron;Hammond, Paula T.
通讯作者：
Hammond, Paula T.
影响因子：
1.1
作者：
Ciocchetta, Federica;Hillston, Jane
通讯作者：
Hillston, Jane
影响因子：
14
作者：
Khoo, Xiaojuan;O'Toole, George A.;Nair, Shrikumar A.;Snyder, Brian D.;Kenan, Daniel J.;Grinstaff, Mark W.
通讯作者：
Grinstaff, Mark W.