Meyer Robert, Obermayer Klaus
Neuroinformatics Group, Department of Software Engineering and Theoretical Computer Science, Technical University BerlinBerlin, Germany; Bernstein Center for Computational NeuroscienceBerlin, Germany.
Neuroinformatics Group, Department of Software Engineering and Theoretical Computer Science, Technical University Berlin Berlin, Germany.
Front Neuroinform. 2016 Aug 25;10:38. doi: 10.3389/fninf.2016.00038. eCollection 2016.
pypet (Python parameter exploration toolkit) is a new multi-platform Python toolkit for managing numerical simulations. Sampling the space of model parameters is a key aspect of simulations and numerical experiments. pypet is designed to allow easy and arbitrary sampling of trajectories through a parameter space beyond simple grid searches. pypet collects and stores both simulation parameters and results in a single HDF5 file. This collective storage allows fast and convenient loading of data for further analyses. pypet provides various additional features such as multiprocessing and parallelization of simulations, dynamic loading of data, integration of git version control, and supervision of experiments via the electronic lab notebook Sumatra. pypet supports a rich set of data formats, including native Python types, Numpy and Scipy data, Pandas DataFrames, and BRIAN(2) quantities. Besides these formats, users can easily extend the toolkit to allow customized data types. pypet is a flexible tool suited for both short Python scripts and large scale projects. pypet's various features, especially the tight link between parameters and results, promote reproducible research in computational neuroscience and simulation-based disciplines.
pypet（Python参数探索工具包）是一个全新的用于管理数值模拟的多平台Python工具包。对模型参数空间进行采样是模拟和数值实验的关键环节。pypet旨在允许通过超出简单网格搜索的参数空间轻松且任意地对轨迹进行采样。pypet会将模拟参数和结果都收集并存储在单个HDF5文件中。这种集中存储方式便于快速且方便地加载数据以进行进一步分析。pypet还提供了各种附加功能，例如模拟的多进程处理和并行化、数据的动态加载、git版本控制的集成以及通过电子实验室笔记本Sumatra对实验进行监督。pypet支持丰富的数据格式集，包括原生Python类型、Numpy和Scipy数据、Pandas数据框以及BRIAN(2)量。除了这些格式外，用户还可以轻松扩展该工具包以支持自定义数据类型。pypet是一个灵活的工具，适用于简短的Python脚本和大规模项目。pypet的各种功能，尤其是参数与结果之间的紧密联系，促进了计算神经科学和基于模拟的学科中的可重复研究。
