RBVI Workshops and Training

The RBVI provides several types of training on the tools we develop, from presentations at conferences to intensive workshops at UCSF or other sites. In addition, many tutorials are available online: [Chimera] [ChimeraX] [Cytoscape] target="_blank">Cytoscape] We often hold workshops at other institutions that have a significant enough user base to make it feasible for us to send a team to the users rather than bringing the users to UCSF. If you are interested in hosting a workshop at your institution, please contact us: rbvi-workshops@cgl.ucsf.edu.

Selected training events are listed below, with links to associated materials where available. See also Selected Presentations.

Event	Date	Topics
NMR and EM experimental methods course, UCSF Biophysics 204A	Dec 11 2017	Using Chimera to compare HSP90 ligands via superposition and hydrogen-bond display [HTML] and to fit HSP90 into a low-resolution map [HTML]
NMR and EM experimental methods course, UCSF Biophysics 204A	Nov 29 2017	Python scripting to create an attribute text file of chemical-shift perturbation values to read into Chimera, then using Chimera to color the HSP90 protein surface by the values [HTML]; ChimeraX virtual reality for ligand visualization
Two-day protein-protein interactions workshop, Max Planck Institute for the Biology of Aging, Cologne, Germany	Nov 27-28 2017	Cytoscape (day 1) and Chimera (day 2); combining network and structural analyses to investigate biological function
ChimeraX demo for light microscopy researchers at UCSF	Oct 5 2017	3D light microscopy data in ChimeraX, measuring distances in mitochondria, cell surface coloring from fluorescent marker, virtual reality
ChimeraX webinar for SBGrid Consortium	Apr 11 2017	Making movies of cryoEM data with UCSF ChimeraX [HTML] [YouTube]
2017 West Coast Protein Crystallography Workshop, Asilomar	Mar 20 2017	Creating animations with UCSF ChimeraX: spin, morph, density fit, and virtual reality movies [HTML]
Cytoscape workshop for the National Cancer Institute, Bethesda	Sep 1-2 2016	Network visualization and analysis
Chimera-Cytoscape workshop at the University of Colorado, Boulder	Aug 15-16 2016	Two-day course covering structure analysis with Chimera and network analysis with Cytoscape
Cytoscape workshop at the University of Southern Denmark, Odense	Jul 29 2016	Introduction to network visualization and analysis
PhD course on protein-protein interactions, Eötvös Loránd University in Budapest, Hungary	Jun 6-7 2016	Two-day course covering both Cytoscape and Chimera; combining network and structural analyses to investigate biological function
Penn State 2016 Bioinorganic Workshop	Jun 5-8 2016	Two 4-hour hands-on workshops on using sequence similarity networks to aid in target selection, analyze metagenomics data, find linker sequences, and explore genomic context
EMBO Practical Course: Computational analysis of protein-protein interactions: Sequences, networks and diseases, Budapest	May 30-Jun 4 2016	Three-hour intro to Chimera, full-day tutorial on network biology and Cytoscape
QCBNet workshop Visualizing & Modeling Cell Biology, Salt Lake City, UT	May 2 2016	Hands-on Chimera tutorial on the visualization and analysis of 3D optical microscopy of crawling cells
Biocuration 2016, Swiss Institute of Bioinformatics, Geneva	Apr 14 2016	Defining functional boundaries within protein similarity networks
Chimera training for UC Berkeley protein engineering course (ChmEng C270/BioE C219)	Nov 20 2015	Intro to Chimera follow-along including basic manipulation, selection-action, H-bond identification, and morphing, then individually working through the structure analysis and comparison tutorial [photo, Tolman Hall computer lab]
EMBO Practical Course: Computational analysis of protein-protein interactions: From sequences to networks, Norwich, UK	Sep 28-Oct 3 2015	3-hour introduction to Chimera and a full-day tutorial on network biology and Cytoscape
Videoconference presentation for graduate course in computational methods, Baylor College of Medicine	Aug 4 2015	Discussion and demonstration of 3D image visualization
Workshop at the University of Copenhagen	Jul 20 2015	Use of Cytoscape, including interactions with UCSF Chimera
23rd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2015), Dublin, Ireland	Jul 11 2015	“Cytoscape 3 App Development: Variations on a theme – Hello World” all-day workshop during which students developed seven apps, each one building on the previous app and utilizing more of the Cytoscape API
Chimera tutorial by Skype to Georgetown University structural biology course	Apr 21 2015	Chimera BLAST searching, morphing, showing MD trajectories, virtual mutation, and rendering; customizing the Chimera interface
UCSF Graduate Programs Minicourse	Apr 21-May 7 2015	Protein function prediction from a big-data perspective using similarity networks
Cytoscape course at UCSF	Apr 7 2015	Introduction to Cytoscape
VIZBI 2015 Visualizing Biological Data Conference at the Broad Institute of MIT and Harvard, Cambridge, MA	Mar 24 2015	Introduction to Chimera tutorial, including visual effects, morphing, making movies, and MultiDomain Assembler