About this Class

Dear colleagues,

The Bioinformatics and Computational Biosciences Branch (BCBB) at NIAID invites you to join us for in-person hands-on workshops that will explore biovisualization techniques. Developers of UCSF ChimeraX and Cytoscape will be on campus for Virtual Reality (VR) 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 the experts from the University of California San Francisco (UCSF)’s Resource for Biocomputing, Visualization, and Informatics (RBVI).

Visit our website for additional information about the workshops and our speakers. 

ALL DAY: Virtual Reality Demonstrations

•    When: 9:30 AM – 4 PM
•    Where: FAES Terrace – 1C168
•    Drop by to explore the molecular structures and medical imaging data in virtual reality with ChimeraX. Hosted by the NIAID Biovisualization Lab. 

Visualizing Atomic Models with ChimeraX

•    When: 1:00 PM – 3:00 PM
•    Where: FAES Classroom 5 - B1C210
•    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. 

Visualizing and Segmenting 3D Medical Imaging Scans

•    When: 1:30 PM – 3:00 PM
•    Where: FAES Classrooms 1 & 2
•    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.

Network Visualization with Cytoscape

•    When: 3:00 PM – 4:30 PM
•    Where: FAES Classroom 5 - B1C210
•    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.

To RSVP for the workshops, please fill out this form. Space in these workshops is limited so we encourage you to sign up now.