Pycellerator: an arrow-based reaction-like modelling language for biological simulations.
Pycellerator: an arrow-based reaction-like modelling language for biological simulations.
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Pycellerator：一种用于生物模拟的基于箭头的类似反应的建模语言。
DOI：
10.1093/bioinformatics/btv596
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发表时间：
2016
期刊：
影响因子：
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通讯作者：
Mjolsness,Eric
中科院分区：
文献类型：
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作者：
Shapiro,BruceE;Mjolsness,Eric
动机：我们介绍了Pycellerator，这是一个Python库，用于从标准文本文件中阅读Cellerator箭头符号，转换为微分方程，生成独立的Python求解器，以及可选地运行和绘制解决方案。所有原始Cellerator箭头，代表从质量作用，Michaeles-Menten-Henri（MMH）和基因调节（GRN）到Monod-Wyman-Changeaux（MWC），用户定义的反应和酶促扩增（KMech）的反应，以前都用Mathematica扩展字符集表示。现在，这些都是ASCII文本文件中的类似反应的命令，由Pycellerator读取，Pycellerator包括一个Python命令行接口（CLI），一个Python应用程序编程接口（API）和一个iPython笔记本接口。结果：Cellerator反应箭头现在输入文本文件中。箭头由Pycellerator解析并转换为Python中的微分方程，Python代码自动生成以求解系统。时间课程是通过执行自动生成的Python代码生成的。用户可以完全自由地修改求解器并使用完整的标准Python工具集。新的库完全独立于旧的Cellerator软件，并且不需要Mathematica。可用性和实施：所有软件都可以从github存储库https://github.com/biomathman/pycellerator/releases获得（GPL）。详细信息，包括安装说明和首字母缩略词和术语的词汇表，在补充信息中给出。联系人：布鲁斯.e.shapiro@csun. edu补充信息：补充数据可在Bioinformaticsonline获得。
Motivation:We introduce Pycellerator, a Python library for reading Cellerator arrow notation from standard text files, conversion to differential equations, generating stand-alone Python solvers, and optionally running and plotting the solutions. All of the original Cellerator arrows, which represent reactions ranging from mass action, Michales–Menten–Henri (MMH) and Gene-Regulation (GRN) to Monod–Wyman–Changeaux (MWC), user defined reactions and enzymatic expansions (KMech), were previously represented with the Mathematica extended character set. These are now typed as reaction-like commands in ASCII text files that are read by Pycellerator, which includes a Python command line interface (CLI), a Python application programming interface (API) and an iPython notebook interface.Results:Cellerator reaction arrows are now input in text files. The arrows are parsed by Pycellerator and translated into differential equations in Python, and Python code is automatically generated to solve the system. Time courses are produced by executing the auto-generated Python code. Users have full freedom to modify the solver and utilize the complete set of standard Python tools. The new libraries are completely independent of the old Cellerator software and do not require Mathematica.Availability and implementation:All software is available (GPL) from the github repository at https://github.com/biomathman/pycellerator/releases. Details, including installation instructions and a glossary of acronyms and terms, are given in the Supplementary information.Contact:bruce.e.shapiro@csun.eduSupplementary information:Supplementary data are available atBioinformaticsonline.