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

中文翻译：

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SBML2Modelica：在开放标准模拟生态系统中集成生化模型

动机：SBML 是定义生化模型的最广泛使用的语言。尽管有数十种 SBML 模拟器可用，但普遍缺乏对 SBML 模型在开放标准通用模拟生态系统中的集成的支持。这阻碍了 SBML 模型在更大的模型网络中的协同仿真和集成，以便例如实现药物、药理学协议或工程人工制品（如生物医学设备）对虚拟生理人体模型的计算机临床试验。Modelica 是最流行的现有开放标准通用仿真语言之一，受到许多仿真器的支持。Modelica 模型特别适用于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）编写的模型可以轻松导出到黑盒功能模型单元 (FMU)，并无缝协同仿真并集成到开放标准语言独立仿真生态系统中的更大模型网络中。结果：为了在异构模型网络中实现 SBML 模型集成，我们提出了 SBML2Modelica，这是一个将 SBML 模型转换为结构良好、用户可理解、易于修改的 Modelica 模型的软件系统。SBML2Modelica 符合 SBML 级别 3 第 2 版，并且在 SBML 测试套件核心的 96.47% 上成功（有一些罕见、复杂且易于避免的结构组合，不受支持并清楚地向用户发出信号）。我们对来自 BioModels 数据库的 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