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RBVI Workshops and Training

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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, there are many online Chimera tutorials and Cytoscape tutorials, some developed for specific workshops, others as standalone materials.

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
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
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
Chimera training for UC Berkeley protein engineering course (ChmEng C270/BioE C219) Nov 21 2014 Intro to Chimera presentation including basic manipulation, selection-action, H-bond identification, morphing, and attributes, followed by hands-on structure analysis and comparison tutorial [photo, Tolman Hall computer lab]
Seventh Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges and Cytoscape Workshops, San Diego Nov 9 2014 Cytoscape developer's workshop
Physical Underpinnings of Biological Systems, UCSF BP205A Oct 21 2014 Showing sequence conservation on structures with Chimera; obtaining a sequence alignment, methods within Chimera for calculating per-column conservation and rendering as colors and/or worms, importing conservation or other values calculated outside of Chimera [HTML]
Macromolecular Interactions course, UCSF BP204 Oct 15 2014 Chimera structural analysis and comparison; contacts and H-bonds, superposition, morphing, viewing sequences, showing attribute values, building multimers, measuring buried surface area
EMBO Practical Course: Computational analysis of protein-protein interactions: From sequences to networks, Cape Town, South Africa Sep 28-Oct 3 2014 Quick introduction to Chimera for molecular visualization (1 hour) and a full-day tutorial on network biology and Cytoscape
Videoconference presentation to “Computational Mathematics for Biomedical Scientists” class, Baylor College of Medicine Sep 25 2014 Chimera visualization and analysis of Ebola virus protein structures and 3D electron microscopy, making movies, finding related structures [HTML]
Penn State Bioinorganic Chemistry Workshop (Bioinformatics section) May 28-Jun 4 2014 Hands-on workshop on using the SFLD and sequence similarity networks
Cytoscape App development course at the European Molecular Biology Laboratory (EMBL) Heidelberg Mar 10-11 2014 Developing apps for the Cytoscape 3.x series; key aspects of the Cytoscape API necessary to manipulate Cytoscape tables, networks, and user interface; setting up development environments
Chimera workshop presented by videoconference to students at the International Institute of Macromolecular Analysis and Nanomedicine Innovation, Taiwan Mar 5 2014 Hands-on introduction to Chimera
Presentations to staff at the European Bioinformatics Institute (EMBL-EBI Hinxton Outstation, Cambridge, UK) Jan 6-11 2014 Approximately 60 hours of meetings including demonstrations of the Structure-Function Linkage Database (SFLD), sequence similarity networks and Pythoscape, troubleshooting issues, and discussing future collaborations
Cytoscape workshop sponsored by the Systems Biology Institute, Melbourne, Australia Oct 28 2013 Analysis and visualization of biological networks; intro to Cytoscape hands-on tutorial; Cytoscape use cases, features in development, and scripting; bring-your-own-data master class
EMBL-Australia Masterclass on Protein Sequence Analysis, Garvan Institute, Sydney, Australia Oct 22-25 2013 Plenary talk on networks and structures, and two sessions each on Cytoscape and Chimera: identifying and understanding protein-protein interactions and residues involved in intermolecular contacts using Cytoscape and structureViz/Chimera; using Chimera for sequence-structure analysis and creating animations
Training at UCSF for members of the Fetrow group (Wake Forest University) Oct 10-11 2013 Using Pythoscape and sequence similarity networks for enzyme superfamily curation
Macromolecular Interactions course, UCSF BP204 Oct 9 2013 Chimera structural analysis and comparison; contacts and H-bonds, superposition, morphing, building multimers, working with sequences
Isoprenoid Synthase Superfamily (ISS) Workshop at UCSF Oct 5 2013 Outreach to the ISS community; curation using sequence similarity networks and the Structure-Function Linkage Database (SFLD)
Visualization and analysis talk via WebEx to first-year graduate students, Baylor College of Medicine Sep 19 2013 Chimera visualization of brain imaging data, molecular structures of nicotinic acetylcholine receptor and alpha-bungarotoxin from krait venom [HTML1] [HTML2]
Cytoscape workshop hosted by California Institute for Quantitative Biosciences (QB3) at UC Berkeley Aug 29 2013 Introduction to Cytoscape network visualization and analysis, use cases, master class
Chimera workshop hosted by California Institute for Quantitative Biosciences (QB3) at UC Berkeley [photo] Aug 27-28 2013 Introduction to Chimera, structure analysis and comparison, sequence-structure tools, EM density analysis, publication images and movies, master class
Chimera tutorial at the University of Dundee Jun 25 2013 Molecular visualization and analysis with Chimera
Enzyme Function Initiative (EFI) meeting, Albert Einstein College of Medicine, New York May 30 2013 Structure-Function Linkage Database (SFLD) representative node networks and Cytoscape
“Computational Tools for Assigning Enzymatic Functions Workshop” at the American Society for Biochemistry and Molecular Biology (ASBMB) annual meeting, Boston, MA Apr 21 2013 Introduction to similarity networks and information available for download from the Structure-Function Linkage Database
Chimera tutorial at VIZBI 2013 (Visualizing Biological Data), Broad Institute, Cambridge, MA Mar 19 2013 Basics of molecular visualization and animation
Webinar for SBGrid Feb 7 2013 Chimera molecular assembly and electron microscopy tools, building a model of alpha-crystallin
Enzyme Mechanisms Meeting Workshop, San Diego, CA Jan 7 2013 Introduction to similarity networks and the Structure-Function Linkage Database


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