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A computational modeling language for complex laboratory experiments

机译：用于复杂实验室实验的计算建模语言

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BioScape~p, a probabilistic version of BioScape, is a new modeling language for a state-dependent stochastic simulation of parallel processes in three dimensional space. Normally a modeling language describes an initial concentration of entities after which all changes are driven by the simulation of reactions. We instead design conditional simulation commands which depend on a global state. Our contribution is a new command in the form when R run A_1…A_n, which will cause A_1…A_n entities to be added to the system when property R in the context of a global state is satisfied. Commands and reactions are further equipped with user-defined update functions to produce side effects on the global state. The global state for simulation is defined to include at least a simulation clock to enable time dependent computation. BioScape~p matches the realistic nature of experimentation, by defining uncertainty from two sources: stochastic movement generating reactions on proximity, and probabilistic choice, where an entity has the ability to be involved in more than one reaction. To capture the richer notion of state dependent conditional commands, which need to be evaluated periodically, we must define a system of multi-level semantics consisting of two layers: World Level Semantics and Individual Level Semantics. Both levels take turns to evaluate their respective domains. The World Level Semantics evaluates the aforementioned when-run conditional commands, while the Individual Level Semantics simulates reactions, entity movement, and maintains the simulation clock and timed entities.
机译：BioScape〜p是概率版本的BioScape，是一种新的建模语言，用于在三维空间中对并行过程进行状态依赖的随机模拟。通常，建模语言描述了实体的初始集中，之后所有变化都由反应的模拟驱动。相反，我们设计依赖于全局状态的条件仿真命令。我们的贡献是以R运行A_1…A_n的形式出现的新命令，当满足全局状态的上下文中的属性R时，这将导致将A_1​​…A_n实体添加到系统中。命令和反应还配备了用户定义的更新功能，以对全局状态产生副作用。用于仿真的全局状态被定义为至少包括仿真时钟，以使得能够进行与时间有关的计算。 BioScape〜p通过定义来自两种来源的不确定性来匹配实验的现实性质：随机运动在邻近区域产生反应，以及概率选择，其中一个实体有能力参与多个反应。为了捕获需要定期评估的状态依赖条件命令的更丰富概念，我们必须定义一个由两层组成的多级语义系统：世界级语义和个人级语义。两个级别轮流评估各自的领域。 “世界级语义”评估上述的运行时条件命令，而“个人级语义”则模拟反应，实体移动并维护模拟时钟和定时实体。

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