Department of Chemistry & Biochemistry, University of Windsor, Windsor, Ontario, Canada.
Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia.
Biophys J. 2021 Nov 2;120(21):4639-4648. doi: 10.1016/j.bpj.2021.09.018. Epub 2021 Sep 24.
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/.
小角 X 射线和中子散射是研究生物膜结构最有力的实验技术之一。对于那些没有时间通过手工分析结果的研究人员，或者对于那些可能缺乏处理此类数据所需的必要科学背景的非专家来说，小角散射（SAS）数据中包含的许多关键信息不容易获取。易于使用的数据可视化软件可以使他们充分利用他们的 SAS 数据，并最大限度地利用有限的资源。为此，我们开发了一个名为 Vesicle Viewer 的基于互联网的应用程序，用于可视化和分析单层脂质双层囊泡的 SAS 数据。Vesicle Viewer 利用了一种称为 EZ-SDP 的经过修改的散射密度分布（SDP）分析，其中易于和稳健地确定关键的双层结构参数，例如每个脂质的面积和双层厚度。值得注意的是，我们引入了一种双层模型，该模型能够描述不对称的双层，无论是化学不对称还是同位素不对称。该应用程序主要使用 Django，这是一个专门用于开发强大的 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来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/ 找到。
