Background

For evaluating the fate of xenobiotics in the environment, a variety of degradation or environmental metabolism experiments are routinely conducted. The data generated in such experiments are evaluated by optimizing the parameters of kinetic models in a way that the model simulation fits the data. No comparison of the main software tools currently in use has been published to date. This article shows a comparison of numerical results as well as an overall, somewhat subjective comparison based on a scoring system using a set of criteria. The scoring was separately performed for two types of uses. Uses of type I are routine evaluations involving standard kinetic models and up to three metabolites in a single compartment. Evaluations involving non-standard model components, more than three metabolites or more than a single compartment belong to use type II. For use type I, usability is most important, while the flexibility of the model definition is most important for use type II.

Results

Test datasets were assembled that can be used to compare the numerical results for different software tools. These datasets can also be used to ensure that no unintended or erroneous behaviour is introduced in newer versions. In the comparison of numerical results, good agreement between the parameter estimates was observed for datasets with up to three metabolites. For the now unmaintained reference software DegKinManager/ModelMaker, and for OpenModel which is still under development, user options were identified that should be taken care of in order to obtain results that are as reliable as possible. Based on the scoring system mentioned above, the software tools gmkin, KinGUII and CAKE received the best scores for use type I. Out of the 15 software packages compared with respect to use type II, again gmkin and KinGUII were the first two, followed by the script based tool mkin, which is the technical basis for gmkin, and by OpenModel.

Conclusions

Based on the evaluation using the system of criteria mentioned above and the comparison of numerical results for the suite of test datasets, the software tools gmkin, KinGUII and CAKE are recommended for use type I, and gmkin and KinGUII for use type II. For users that prefer to work with scripts instead of graphical user interfaces, mkin is recommended. For future software evaluations, it is recommended to include a measure for the total time that a typical user needs for a kinetic evaluation into the scoring scheme. It is the hope of the authors that the publication of test data, source code and overall rankings foster the evolution of useful and reliable software in the field.

中文翻译：

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化学降解数据动力学评估软件工具的比较。

背景

为了评估外源物质在环境中的命运，通常进行各种降解或环境代谢实验。通过以模型模拟拟合数据的方式优化动力学模型的参数来评估此类实验中生成的数据。迄今为止，尚未发布目前使用的主要软件工具的比较。本文展示了数值结果的比较，以及基于使用一组标准的评分系统的总体、有些主观的比较。分别针对两种类型的用途进行评分。I 型的用途是涉及标准动力学模型和单个隔室中最多三种代谢物的常规评估。涉及非标准模型成分、超过三个代谢物或超过单个隔室的评估属于使用类型II。对于使用类型 I，可用性最重要，而模型定义的灵活性对于使用类型 II 最重要。

结果

组装了测试数据集，可用于比较不同软件工具的数值结果。这些数据集还可用于确保新版本中不会引入意外或错误的行为。在数值结果的比较中，对于最多含有三种代谢物的数据集，观察到参数估计值之间具有良好的一致性。对于现在未维护的参考软件 DegKinManager/ModelMaker 以及仍在开发中的 OpenModel，已确定应注意的用户选项，以便获得尽可能可靠的结果。根据上述评分系统，软件工具 gmkin、KinGUII 和 CAKE 在使用类型 I 方面获得了最高分数。在与使用类型 II 进行比较的 15 个软件包中，gmkin 和 KinGUII 再次排名前两名，其次是基于脚本的工具 mkin，它是 gmkin 的技术基础，由 OpenModel 提供。

结论

根据上述标准体系的评估以及测试数据集数值结果的比较，推荐使用软件工具gmkin、KinGUII和CAKE作为I类，gmkin和KinGUII作为II类。对于喜欢使用脚本而不是图形用户界面的用户，建议使用 mkin。对于未来的软件评估，建议将典型用户进行动力学评估所需的总时间纳入评分方案中。作者希望测试数据、源代码和总体排名的发布能够促进该领域有用且可靠的软件的发展。