WebCM:一个基于Web的平台,用于多用户基于个体的多细胞微生物群体和社区的建模
Jason Philippou1, Guillermo Yáñez Feliú1, Timothy J Rudge1
1Interdisciplinary Computing and Complex Biosystems, School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.
ACS synthetic biology
|May 14, 2024
概括
WebCM是一个用于创建和运行微生物群体模拟的网络平台. 它提供3D可视化,并通过云或本地服务器部署支持协作研究.
科学领域:
- 微生物学 微生物学
- 计算生物学 计算生物学
- 生物信息学是一种生物信息学.
背景情况:
- 微生物种群动态复杂,需要先进的模拟工具.
- 现有的模拟软件往往缺乏用户友好的界面和协作功能.
- 基于Web的平台可以提高计算生物学中的可访问性和协作.
研究的目的:
- 介绍WebCM,这是一个新的网络平台,用于基于个体的微生物种群模拟.
- 为创建,编辑,运行和可视化模拟提供一个用户友好的,基于浏览器的界面.
- 利用现有的模拟软件 (CellModeller) 在远程服务器上进行高效的计算.
主要方法:
- WebCM使用CellModeller软件进行后端模拟.
- 它使用web浏览器界面进行模型编辑,执行和播放.
- 该平台支持同时多用户访问和管理多个模拟.
- 它利用GPU和CPU并行实现计算效率.
主要成果:
- WebCM可以实时实现模拟的交互式3D图形表示.
- 用户可以在所有时间点检查模拟,并下载结果进行离线分析.
- 该平台通过允许共享对计算资源的访问来促进协作研究.
- 可以在云服务或本地服务器上部署WebCM.
结论:
- WebCM为微生物种群和社区模拟提供了一个可访问和强大的平台.
- 基于Web的界面和协作功能增强了计算建模的可用性和影响.
- 通过整合CellModeller,WebCM提供了高效的模拟功能与并行处理.
- 该平台支持个人实验室使用和实验室间协作.
相关概念视频
01:18Imaging Biological Samples with Optical Microscopy
Optical microscopy uses optic principles to provide detailed images of samples. Antonie van Leeuwenhoek designed the first compound optical microscope in the 17th century to visualize blood cells, bacteria, and yeast cells. In 1830, Joseph Jackson Lister created an essentially modern light microscope. The 20th century saw the development of microscopes with enhanced magnification and resolution.
In optical microscopy, the specimen to be viewed is placed on a glass slide and clipped on the stage...
In optical microscopy, the specimen to be viewed is placed on a glass slide and clipped on the stage...
01:29Two-Dimensional Microscopy in Microbiology
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01:28Three-Dimensional Microscopy in Microbiology
Three-dimensional imaging techniques are essential in cell biology, allowing researchers to visualize intricate cellular structures with high resolution. Two prominent methods, Differential Interference Contrast Microscopy (DIC) and Confocal Scanning Laser Microscopy (CSLM), provide distinct advantages for imaging live and thick specimens, respectively.Differential Interference Contrast MicroscopyDIC microscopy enhances contrast in transparent, unstained samples by converting phase...
01:29Microbial Morphologies
Bacterial and archaeal cells exhibit remarkable diversity in shape and structure, critical in their adaptability and functionality. Among bacteria, the most commonly observed shapes include cocci and bacilli. Cocci are spherical and may exist singly or in groupings such as pairs (diplococci), chains (streptococci), clusters (staphylococci), or tetrads. Bacilli, in contrast, are rod-shaped and can also occur as single cells, in pairs, or chains, depending on their environmental and genetic...