论文标题
libroadrunner 2.0：高性能的SBML模拟和分析库
libRoadRunner 2.0: A High-Performance SBML Simulation and Analysis Library
论文作者
论文摘要
动机：本文介绍了libroadrunner 2.0，这是一种可扩展的，高性能的，跨平台的开源软件库，用于使用Systems Biology Markup语言SBML表示模型的仿真和分析）。 结果：libroadrunner是一个独立的库，能够通过其C ++和C绑定在其他工具中作为组件运行，并通过其Python或Julia界面进行交互性。 Libroadrunner使用的定制即时JIT编译器建立在广泛使用的LLVM JIT编译器框架上。它将SBML指定的模型直接编译为各种处理器的本机机器代码，使其适合于解决极大的模型或重复运行。 LibRoadRunner具有灵活性，支持SBML规范的大部分（延迟和非线性代数方程除外），并包括几个SBML扩展，例如组成和分布。它提供了多个确定性和随机集成剂，以及用于化学计量矩阵的稳态，灵敏度，稳定性分析和结构分析的工具。 可用性：LibroadRunner二进制分布可用于Mac OS X，Linux和Windows。该库是根据Apache许可证2.0版获得许可的。 Libroadrunner也可用于基于ARM的计算机，例如Raspberry Pi，可以原则上根据LLVM-13支持的任何系统进行编译。 http://sys-bio.github.io/RoadRunner/index.html提供在线文档，完整的构建说明，二进制文件和git源存储库。
Motivation: This paper presents libRoadRunner 2.0, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language SBML). Results: libRoadRunner is a self-contained library, able to run both as a component inside other tools via its C++ and C bindings, and interactively through its Python or Julia interface. libRoadRunner uses a custom Just-In-Time JIT compiler built on the widely-used LLVM JIT compiler framework. It compiles SBML-specified models directly into native machine code for a large variety of processors, making it appropriate for solving extremely large models or repeated runs. libRoadRunner is flexible, supporting the bulk of the SBML specification (except for delay and nonlinear algebraic equations) and including several SBML extensions such as composition and distributions. It offers multiple deterministic and stochastic integrators, as well as tools for steady-state, sensitivity, stability analysis, and structural analysis of the stoichiometric matrix. Availability: libRoadRunner binary distributions are available for Mac OS X, Linux, and Windows. The library is licensed under the Apache License Version 2.0. libRoadRunner is also available for ARM-based computers such as the Raspberry Pi and can in principle be compiled on any system supported by LLVM-13. http://sys-bio.github.io/roadrunner/index.html provides online documentation, full build instructions, binaries, and a git source repository.
