On February 21, the NIAID Bioinformatics and Computational Biosciences Branch (BCBB) will host developers of UCSF ChimeraX and Cytoscape for Virtual Reality demos and in-person hands-on workshops. These will showcase the use of ChimeraX for visualizing and analyzing 3D medical imaging scans and 3D molecular structures, and Cytoscape for network visualization. These immersive experiences will be led by experts from the University of California San Francisco (UCSF)’s Resource for Biocomputing, Visualization, and Informatics (RBVI) .
For questions and information, please contact 3D@nih.gov .
Drop by to explore molecular structures and medical imaging data in virtual reality with ChimeraX. Hosted by the NIAID Biovisualization Lab.
This hands-on session will introduce visualizing atomic models, X-ray maps, cryoEM maps, AlphaFold models, and NMR constraints using ChimeraX 1.7. Developed by UCSF, ChimeraX is an open-source next-generation molecular visualization program.
This course is suitable for anyone who is new to using the UCSF ChimeraX application. Experienced users of ChimeraX (and Chimera) may benefit from instruction on the newest features in ChimeraX.
Please install ChimeraX 1.7.1 onto your laptop before bringing it to the workshop. You can obtain it here: https://www.cgl.ucsf.edu/chimerax/download.html
The workshop materials are available for preview here: https://www.rbvi.ucsf.edu/chimerax/data/methods-jan2024/methods.html
In this tutorial, we’ll learn how to use UCSF ChimeraX to look at a variety of medical image formats. Over the past few years, ChimeraX has been increasingly integrating medical image analysis alongside its traditional use case as a molecular visualization tool. We’ll go over those advancements in our program, first by getting our bearings loading publicly accessible anonymized images from the Cancer Imaging Archive. Using that data, we’ll explore different ways to customize the look of the data in ChimeraX. Finally, we’ll use newly developed tools for visualization and segmentation including interactive segmentation in virtual reality.
Please install ChimeraX 1.7.1 onto your laptop before bringing it to the workshop. You can obtain it here: https://www.cgl.ucsf.edu/chimerax/download.html
In this tutorial, we will explore the network analysis and visualization tool Cytoscape. Cytoscape is an excellent tool to create effective network figures, integrate public network and pathway sources (e.g. STRING, NDex, IntAct, Reactome, Wikipathways) with your own proteomic or transcriptomic data. During the tutorial, we'll talk about how to load data from public sources, integrate data, and some tips and tricks for visualizing your networks. This will be a hands-on tutorial, so please bring your laptop with Cytoscape 3.10.1 loaded.
You can obtain Cytoscape here: https://cytoscape.org/download.html
Instructor: Tom Goddard. Tom develops ChimeraX software capabilities for AlphaFold structure prediction, cryoEM maps, and virtual reality visualization of molecules at UC San Francisco.
Instructor: Zach Pearson. Zach is a software engineer at the Resource for Biocomputing, Visualization, and Informatics at UCSF and a member of the UCSF ChimeraX development team. Since joining the RBVI, he has taken point on building out ChimeraX’s capabilities in the medical imaging space and is the primary developer of the tools being shown in this tutorial.
Instructor: John "Scooter" Morris, Ph.D. Scooter is the Executive Director of the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco. He is also an Adjunct Assistant Professor in the department of Pharmaceutical Chemistry. Scooter is the author of over 50 peer-reviewed publications and is a member of the Cytoscape core development team. Scooter also serves as the "Roving Engineer" for the Cytoscape project and is the author of over two dozen Cytoscape apps, including the stringApp and clusterMaker2.