Vesicle Viewer: Online visualization and analysis of small-angle scattering from lipid vesicles
Vesicle Viewer: Online visualization and analysis of small-angle scattering from lipid vesicles
复制标题
囊泡查看器：脂质囊泡小角度散射的在线可视化和分析
DOI：
10.1016/j.bpj.2021.09.018
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发表时间：
2021
影响因子：
3.4
通讯作者：
Marquardt, Drew
中科院分区：
文献类型：
--
作者：
Lewis-Laurent, Aislyn;Doktorova, Milka;Heberle, Frederick A.;Marquardt, Drew
小角X射线和中子散射是研究生物膜结构的最有力的实验技术之一。小角散射（SAS）数据中包含的许多关键信息对于研究人员来说并不容易获得，因为他们的时间有限，无法手工分析结果，或者对于可能缺乏必要科学背景来处理此类数据的非专家来说也不容易获得。易于使用的数据可视化软件可以让他们充分利用SAS数据，最大限度地利用有限的资源。为此，我们开发了一个基于互联网的应用程序，称为囊泡查看器可视化和分析SAS数据从单层脂质双层囊泡。Vesicle Viewer利用称为EZ-SDP的修改散射密度分布（SDP）分析，其中可以轻松且稳健地确定关键的双层结构参数，例如单位脂质面积和双层厚度。值得注意的是，我们引入了一个双层模型，能够描述一个不对称的双层，无论是化学或同位素不对称。该应用程序主要使用Django，这是一个专门用于开发健壮的Web应用程序的Python包。此外，还使用了其他几个库来支持项目的更多技术方面;值得注意的例子是Matplotlib（用于图形）和NumPy（用于计算）。通过消除下载和安装软件的障碍，这个基于网络的应用程序将允许科学家使用他们喜欢的操作系统分析他们自己的囊泡散射数据。基于网络的应用程序可以在https://vesicleviewer.dmarquardt.ca/上找到。
Small-angle X-ray and neutron scattering are among the most powerful experimental techniques for investigating the structure of biological membranes. Much of the critical information contained in small-angle scattering (SAS) data is not easily accessible to researchers who have limited time to analyze results by hand or to nonexperts who may lack the necessary scientific background to process such data. Easy-to-use data visualization software can allow them to take full advantage of their SAS data and maximize the use of limited resources. To this end, we developed an internet-based application called Vesicle Viewer to visualize and analyze SAS data from unilamellar lipid bilayer vesicles. Vesicle Viewer utilizes a modified scattering density profile (SDP) analysis called EZ-SDP in which key bilayer structural parameters, such as area per lipid and bilayer thickness, are easily and robustly determined. Notably, we introduce a bilayer model that is able to describe an asymmetric bilayer, whether it be chemically or isotopically asymmetric. The application primarily uses Django, a Python package specialized for the development of robust web applications. In addition, several other libraries are used to support the more technical aspects of the project; notable examples are Matplotlib (for graphs) and NumPy (for calculations). By eliminating the barrier of downloading and installing software, this web-based application will allow scientists to analyze their own vesicle scattering data using their preferred operating system. The web-based application can be found at https://vesicleviewer.dmarquardt.ca/.