PyChelator：一个基于 Python 的 Colab 和网络应用程序，用于金属螯合剂计算。

PyChelator: a Python-based Colab and web application for metal chelator calculations.

机构信息

Institute of Molecular and Cell Physiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.

Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada.

出版信息

BMC Bioinformatics. 2024 Jul 16;25(1):239. doi: 10.1186/s12859-024-05858-8.

DOI:10.1186/s12859-024-05858-8

PMID:39014298

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11253343/

Abstract

BACKGROUND

Metal ions play vital roles in regulating various biological systems, making it essential to control the concentration of free metal ions in solutions during experimental procedures. Several software applications exist for estimating the concentration of free metals in the presence of chelators, with MaxChelator being the easily accessible choice in this domain. This work aimed at developing a Python version of the software with arbitrary precision calculations, extensive new features, and a user-friendly interface to calculate the free metal ions.

RESULTS

We introduce the open-source PyChelator web application and the Python-based Google Colaboratory notebook, PyChelator Colab. Key features aim to improve the user experience of metal chelator calculations including input in smaller units, selection among stability constants, input of user-defined constants, and convenient download of all results in Excel format. These features were implemented in Python language by employing Google Colab, facilitating the incorporation of the calculator into other Python-based pipelines and inviting the contributions from the community of Python-using scientists for further enhancements. Arbitrary-precision arithmetic was employed by using the built-in Decimal module to obtain the most accurate results and to avoid rounding errors. No notable differences were observed compared to the results obtained from the PyChelator web application. However, comparison of different sources of stability constants showed substantial differences among them.

CONCLUSIONS

PyChelator is a user-friendly metal and chelator calculator that provides a platform for further development. It is provided as an interactive web application, freely available for use at https://amrutelab.github.io/PyChelator , and as a Python-based Google Colaboratory notebook at https://colab.

RESEARCH

google.com/github/AmruteLab/PyChelator/blob/main/PyChelator_Colab.ipynb .

摘要

背景

金属离子在调节各种生物系统中起着至关重要的作用，因此在实验过程中控制溶液中游离金属离子的浓度至关重要。目前有几种软件应用程序可用于估计螯合剂存在时游离金属的浓度，其中 MaxChelator 是该领域易于使用的选择。本工作旨在开发具有任意精度计算、广泛新功能和用户友好界面的软件的 Python 版本，以计算游离金属离子。

结果

我们引入了开源的 PyChelator 网络应用程序和基于 Python 的 Google Colaboratory 笔记本，即 PyChelator Colab。旨在改善金属螯合剂计算的用户体验的关键功能包括以较小的单位输入、在稳定性常数之间进行选择、输入用户定义的常数以及以 Excel 格式方便地下载所有结果。这些功能是通过使用 Google Colab 以 Python 语言实现的，便于将计算器集成到其他基于 Python 的管道中，并邀请使用 Python 的科学家社区为进一步增强功能做出贡献。通过使用内置的 Decimal 模块进行任意精度算术运算，可以获得最准确的结果并避免舍入误差。与从 PyChelator 网络应用程序获得的结果相比，没有观察到明显的差异。然而，比较不同稳定性常数的来源表明它们之间存在很大差异。

结论

PyChelator 是一款用户友好的金属和螯合剂计算器，为进一步开发提供了平台。它作为交互式网络应用程序提供，可免费在 https://amrutelab.github.io/PyChelator 上使用，并作为基于 Python 的 Google Colaboratory 笔记本在 https://colab.上提供。