Smoldyn 模拟器的 Python 接口。
Python interfaces for the Smoldyn simulator.
机构信息
Subconscious Compute Pvt. Ltd., Bangalore, Karnataka 560064, India.
Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
出版信息
Bioinformatics. 2021 Dec 22;38(1):291-293. doi: 10.1093/bioinformatics/btab530.
MOTIVATION
Smoldyn is a particle-based biochemical simulator that is frequently used for systems biology and biophysics research. Previously, users could only define models using text-based input or a C/C++ application programming interface (API), which were convenient, but limited extensibility.
RESULTS
We added a Python API to Smoldyn to improve integration with other software tools, such as Jupyter notebooks, other Python code libraries and other simulators. It includes low-level functions that closely mimic the existing C/C++ API and higher-level functions that are more convenient to use. These latter functions follow modern object-oriented Python conventions.
AVAILABILITY AND IMPLEMENTATION
Smoldyn is open source and free, available at http://www.smoldyn.org and can be installed with the Python package manager pip. It runs on Mac, Windows and Linux.
UNLABELLED
Documentation is available at http://www.smoldyn.org/SmoldynManual.pdf and https://smoldyn.readthedocs.io/en/latest/python/api.html.
动机
Smoldyn 是一款基于粒子的生化模拟器，常用于系统生物学和生物物理学研究。此前，用户只能使用基于文本的输入或 C/C++应用程序编程接口 (API) 来定义模型，虽然这很方便，但可扩展性有限。
结果
我们为 Smoldyn 添加了 Python API，以提高与其他软件工具（如 Jupyter 笔记本、其他 Python 代码库和其他模拟器）的集成度。它包括紧密模拟现有 C/C++ API 的低级函数，以及更便于使用的高级函数。这些后一类函数遵循现代面向对象的 Python 约定。
可用性和实现
Smoldyn 是开源且免费的，可在 http://www.smoldyn.org 上获得，并可通过 Python 包管理器 pip 进行安装。它可在 Mac、Windows 和 Linux 上运行。
未标记
文档可在 http://www.smoldyn.org/SmoldynManual.pdf 和 https://smoldyn.readthedocs.io/en/latest/python/api.html 上获得。
Zotero 插件