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IOCBIO Kinetics: An open-source software solution for analysis of data traces
PLOS Computational Biology ( IF 4.3 ) Pub Date : 2020-12-22 , DOI: 10.1371/journal.pcbi.1008475
Marko Vendelin , Martin Laasmaa , Mari Kalda , Jelena Branovets , Niina Karro , Karina Barsunova , Rikke Birkedal

Biological measurements frequently involve measuring parameters as a function of time, space, or frequency. Later, during the analysis phase of the study, the researcher splits the recorded data trace into smaller sections, analyzes each section separately by finding a mean or fitting against a specified function, and uses the analysis results in the study. Here, we present the software that allows to analyze these data traces in a manner that ensures repeatability of the analysis and simplifies the application of FAIR (findability, accessibility, interoperability, and reusability) principles in such studies. At the same time, it simplifies the routine data analysis pipeline and gives access to a fast overview of the analysis results. For that, the software supports reading the raw data, processing the data as specified in the protocol, and storing all intermediate results in the laboratory database. The software can be extended by study- or hardware-specific modules to provide the required data import and analysis facilities. To simplify the development of the data entry web interfaces, that can be used to enter data describing the experiments, we released a web framework with an example implementation of such a site. The software is covered by open-source license and is available through several online channels.



中文翻译:

IOCBIO Kinetics:用于数据跟踪分析的开源软件解决方案

生物测量经常涉及根据时间,空间或频率测量参数。后来,在研究的分析阶段,研究人员将记录的数据迹线分成较小的部分,通过查找均值或针对指定函数进行拟合分别分析每个部分,并在研究中使用分析结果。在这里,我们介绍了一种软件,该软件可以确保分析的可重复性并简化FAIR(查找性,可访问性,互操作性和可重用性)原理在此类研究中的应用,从而分析这些数据轨迹。同时,它简化了常规数据分析流程,并提供了对分析结果的快速概述。为此,该软件支持读取原始数据,按照协议中的规定处理数据,并将所有中间结果存储在实验室数据库中。该软件可以通过特定于研究或硬件的模块进行扩展,以提供所需的数据导入和分析工具。为了简化数据输入Web界面的开发(可用于输入描述实验的数据),我们发布了一个Web框架,并提供了此类网站的示例实现。该软件受开放源代码许可保护,可以通过几个在线渠道获得。我们发布了一个包含此类网站的示例实现的网络框架。该软件受开放源代码许可保护,可以通过几个在线渠道获得。我们发布了一个包含此类网站的示例实现的网络框架。该软件受开放源代码许可保护,可以通过几个在线渠道获得。

更新日期:2020-12-22
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