Petri nets are a common method for modeling and simulation of systems biology application cases. Usually different Petri net concepts (e.g. discrete, hybrid, functional) are demanded depending on the purpose of the application cases. Modeling complex application cases requires a unification of those concepts, e.g. hybrid functional Petri nets (HFPN) and extended hybrid Petri nets (xHPN). Existing tools have certain limitations which motivated the extension of VANESA, an existing open-source editor for biological networks. The extension can be used to model, simulate, and visualize Petri nets based on the xHPN formalism. Moreover, it comprises additional functionality to support and help the user. Complex (kinetic) functions are syntactically analyzed and mathematically rendered. Based on syntax and given physical unit information, modeling errors are revealed. The numerical simulation is seamlessly integrated and executed in the background by the open-source simulation environment OpenModelica utilizing the Modelica library PNlib. Visualization of simulation results for places, transitions, and arcs are useful to investigate and understand the model and its dynamic behavior. The impact of single parameters can be revealed by comparing multiple simulation results. Simulation results, charts, and entire specification of the Petri net model as Latex file can be exported. All these features are shown in the demonstration case. The utilized Petri net formalism xHPN is fully specified and implemented in PNlib. This assures transparency, reliability, and comprehensible simulation results. Thus, the combination of VANESA and OpenModelica shape a unique open-source Petri net environment focusing on systems biology application cases. VANESA is available at: http://agbi.techfak.uni-bielefeld.de/vanesa.

Petri 网是对系统生物学应用案例进行建模和仿真的常用方法。根据应用案例的目的，通常需要不同的 Petri 网概念（例如离散的、混合的、功能的）。对复杂应用案例建模需要统一这些概念，例如混合功能 Petri 网 (HFPN) 和扩展混合 Petri 网 (xHPN)。现有的工具有一定的局限性，这激发了 VANESA 的扩展，VANESA 是一个现有的生物网络开源编辑器。该扩展可用于基于 xHPN 形式对 Petri 网进行建模、模拟和可视化。此外，它还包含支持和帮助用户的附加功能。复杂（动力学）函数经过句法分析和数学渲染。基于语法和给定的物理单元信息，模型错误暴露出来。数值模拟通过使用 Modelica 库 PNlib 的开源模拟环境 OpenModelica 在后台无缝集成和执行。位置、过渡和弧线的仿真结果可视化有助于研究和理解模型及其动态行为。通过比较多个模拟结果可以揭示单个参数的影响。可以将 Petri 网模型的模拟结果、图表和整个规范导出为 Latex 文件。所有这些功能都显示在演示案例中。所使用的 Petri 网形式主义 xHPN 在 PNlib 中完全指定和实现。这确保了透明度、可靠性和可理解的模拟结果。因此，VANESA 和 OpenModelica 的结合形成了一个专注于系统生物学应用案例的独特的开源 Petri 网环境。VANESA 可在以下网址获得：http://agbi.techfak.uni-bielefeld.de/vanesa。