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Pycellerator: an arrow-based reaction-like modelling language for biological simulations

机译:Pycellerator:一种用于生物模拟的基于箭头的类似反应的建模语言

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摘要

>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 . Details, including installation instructions and a glossary of acronyms and terms, are given in the .>Contact: >Supplementary information: are available at Bioinformatics online.
机译:>动机:我们引入了Pycellerator,这是一个Python库,用于从标准文本文件中读取Cellerator箭头符号,转换为微分方程,生成独立的Python解算器,以及可选地运行和绘制解法。最初的Cellerator箭头代表反应,包括质量作用,Michales-Menten-Henri(MMH)和基因调控(GRN)到Monod-Wyman-Changeaux(MWC),用户定义的反应和酶促扩展(KMech),以前用Mathematica扩展字符集表示。现在,这些字符在Pycellerator读取的ASCII文本文件中被键入为类似反应的命令,其中包括Python命令行界面(CLI),Python应用程序编程界面(API)和iPython Notebook界面。>结果:< / strong>现在在文本文件中输入了Cellerator反应箭头。箭头由Pycellerator解析并转换为Python中的微分方程,然后自动生成Python代码来求解系统。时间课程是通过执行自动生成的Python代码产生的。用户拥有完全的自由来修改求解器并使用完整的标准Python工具集。新库完全独立于旧的Cellerator软件,不需要Mathematica。>可用性和实现:所有软件(GPL)可从github上的github存储库获得。有关详细信息,包括安装说明以及首字母缩写词和术语的词汇表,请参见。>联系方式: >补充信息:可从在线生物信息学获得。

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