SBML2Modelica：在开放标准模拟生态系统中集成生物化学模型
SBML2Modelica: integrating biochemical models within open-standard simulation ecosystems
摘要：
动机：SBML是定义生物化学模型的最广泛的语言。虽然有几十个SBML模拟器可用，但在开放标准的通用模拟生态系统中，普遍缺乏对SBML模型集成的支持。这阻碍了SBML模型在更大的模型网络中的协同仿真和集成，以便例如能够针对虚拟生理人体模型进行药物、药理学协议或工程人工制品（例如生物医学设备）的计算机临床试验。Modelica是现有最流行的开放标准通用仿真语言之一，受到许多仿真器的支持。Modelica模型特别适合定义几乎所有应用领域的异构模型的复杂网络。用Modelica（以及100多种其他语言）编写的模型可以很容易地导出到黑盒功能模型单元（FMU）中，并在开放标准的独立于语言的仿真生态系统中无缝地协同仿真和集成到更大的模型网络中。结果如下：为了使SBML模型集成在异构模型网络，我们提出SBML2Modelica，一个软件系统转换SBML模型到结构良好，用户可理解的，易于修改的Modelica模型。SBML2Modelica符合SBML Level 3 Version 2标准，并在SBML Test Suite Core上成功实现了96.47%的成功率（少数罕见、复杂且容易避免的结构组合不受支持，并清晰地向用户发出信号）。我们对BioModels数据库中的613个模型（最多5438个变量）进行的实验表明，主要的开源（通用）Modelica和FMU模拟器的性能可与最先进的专业SBML模拟器相媲美。可用性和实施：https://bitbucket.org/mclab/sbml2modelica
英文摘要：
Motivation: SBML is the most widespread language for the definition of biochemical models. Although dozens of SBML simulators are available, there is a general lack of support to the integration of SBML models within open-standard general-purpose simulation ecosystems. This hinders co-simulation and integration of SBML models within larger model networks, in order to, e.g. enable in silico clinical trials of drugs, pharmacological protocols, or engineering artefacts such as biomedical devices against Virtual Physiological Human models. Modelica is one of the most popular existing open-standard general-purpose simulation languages, supported by many simulators. Modelica models are especially suited for the definition of complex networks of heterogeneous models from virtually all application domains. Models written in Modelica (and in 100+ other languages) can be readily exported into black-box Functional Mock-Up Units (FMUs), and seamlessly co-simulated and integrated into larger model networks within open-standard language-independent simulation ecosystems. Results: In order to enable SBML model integration within heterogeneous model networks, we present SBML2Modelica, a software system translating SBML models into well-structured, user-intelligible, easily modifiable Modelica models. SBML2Modelica is SBML Level 3 Version 2-compliant and succeeds on 96.47% of the SBML Test Suite Core (with a few rare, intricate and easily avoidable combinations of constructs unsupported and cleanly signalled to the user). Our experimental campaign on 613 models from the BioModels database (with up to 5438 variables) shows that the major open-source (general-purpose) Modelica and FMU simulators achieve performance comparable to state-of-the-art specialized SBML simulators. Availability and implementation: https://bitbucket.org/mclab/sbml2modelica
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
