Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10-12, 08028 Barcelona, Spain.
Barcelona Supercomputing Center (BSC), Jordi Girona 29, 08034, Barcelona, Spain.
Nucleic Acids Res. 2022 Jul 5;50(W1):W99-W107. doi: 10.1093/nar/gkac380.
We present BioExcel Building Blocks Workflows, a web-based graphical user interface (GUI) offering access to a collection of transversal pre-configured biomolecular simulation workflows assembled with the BioExcel Building Blocks library. Available workflows include Molecular Dynamics setup, protein-ligand docking, trajectory analyses and small molecule parameterization. Workflows can be launched in the platform or downloaded to be run in the users' own premises. Remote launching of long executions to user's available High-Performance computers is possible, only requiring configuration of the appropriate access credentials. The web-based graphical user interface offers a high level of interactivity, with integration with the NGL viewer to visualize and check 3D structures, MDsrv to visualize trajectories, and Plotly to explore 2D plots. The server requires no login but is recommended to store the users' projects and manage sensitive information such as remote credentials. Private projects can be made public and shared with colleagues with a simple URL. The tool will help biomolecular simulation users with the most common and repetitive processes by means of a very intuitive and interactive graphical user interface. The server is accessible at https://mmb.irbbarcelona.org/biobb-wfs.
我们展示了 BioExcel Building Blocks Workflows,这是一个基于网络的图形用户界面 (GUI),提供了对一系列横向预配置的生物分子模拟工作流程的访问,这些工作流程是使用 BioExcel Building Blocks 库组装的。可用的工作流程包括分子动力学设置、蛋白质-配体对接、轨迹分析和小分子参数化。工作流程可以在平台上启动,也可以下载到用户自己的场所运行。可以远程将长时间的执行操作启动到用户可用的高性能计算机上,只需配置适当的访问凭据即可。基于网络的图形用户界面提供了高度的交互性,与 NGL 查看器集成,用于可视化和检查 3D 结构,与 MDsrv 集成,用于可视化轨迹,与 Plotly 集成,用于探索 2D 图。该服务器不需要登录,但建议用于存储用户的项目和管理敏感信息,如远程凭据。私人项目可以通过简单的 URL 公开并与同事共享。该工具将通过非常直观和交互的图形用户界面帮助生物分子模拟用户处理最常见和重复的过程。该服务器可在 https://mmb.irbbarcelona.org/biobb-wfs 访问。