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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 holds 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
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
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
Chimera hands-on tutorial at UC Berkeley Dec 19 2012 Map segmentation: surface masking, watershed segmentation, zones around markers and atoms
2012 Cytoscape retreat, Gladstone Institutes, UCSF Dec 13 2012 Hands-on tutorial: Cytoscape network visualization and analysis
Chimera hands-on tutorial at UC Berkeley Dec 5 2012 Basic molecular display, segmenting and fitting single-particle density maps, extracting regions from termite gut FIBSEM data
Northern California Society for Microscopy meeting, UCSF Nov 15 2012 Viewing and analyzing microscopy data with Chimera; map segmentation [HTML]
Macromolecular Interactions course, UCSF BP204 Oct 17 2012 Chimera structural analysis and comparison; contacts and H-bonds, superposition, morphing, building multimers, working with sequences
Introduction to Bioinformatics course, UCSF BMI206 Oct 14-30 2012 Four hours of lecture featuring superfamily analysis, protein similarity networks, and the Structure-Function Linkage Database, which was also used in a lab assignment
Cytoscape workshop at NIH, Bethesda, MD Oct 4 2012 Network visualization and analysis with Cytoscape [workshop materials]
Chimera workshop at NIH, Bethesda, MD Oct 2-3 2012 Introduction to Chimera, structure analysis, sequence-structure tools, EM density analysis, publication images and movies [workshop materials]
Workshop on the Radical SAM Superfamily, UCSF Sep 29 2012 Radical SAM superfamily curation and analysis with the Structure-Function Linkage Database
Bay Area cryo-EM meeting, Santa Cruz Aug 27 2012 Making movies in Chimera, morphing EM maps and molecular structures of ParM [HTML]
Chimera training via WebEx for graduate students in structural and computational biology, Baylor College of Medicine Aug 14 2012 Chimera visualization of protein structures and sequences (dipeptide epimerase) and covering multiple length scales, from atoms to cells (T-cell tomography and termite gut EM)
Chimera hands-on training by teleconference, cryoEM workshop at the National University of Singapore Jul 12 2012 Electron tomography segmentation, molecule display, fitting; Q & A [HTML]
Chimera training for the DeGrado group at UCSF Jul 3 2012 Chimera structural analysis and comparison; H-bonds, superposition, morphing, attributes, working with sequences, density display, making movies; Q & A
Chimera workshop at the University of Missouri Apr 28 2012 Molecular visualization and analysis
Cytoscape workshop at the University of Missouri Apr 27 2012 Network visualization and analysis
Cytoscape tutorial at the Swiss Institute of Bioinformatics, Lausanne Mar 12-13 2012 Network visualization and analysis
Chimera tutorial at VIZBI 2012 (EMBO Visualizing Biological Data conference), Heidelberg, Germany Mar 5 2012 Basics of molecular visualization and animation
Cytoscape developer tutorial at VIZBI 2012, Heidelberg, Germany Mar 5 2012 Cytoscape plugin development


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