--------------------------------------------------------------------------- "Outreach and Training" activities for RBVI annual report and competitive grant renewals This wiki encompasses all RBVI outreach and training activities, not just those related to Chimera. The overall goal of the training component of the RBVI is twofold: to improve the general understanding of our technologies in the appropriate population and to create a cadre of biomedical researchers trained in the technology so that they can effectively apply it in their own research. Each entry below should include the following: * Title of event (e.g., EMBO electron microscopy workshop) * Nature of training (e.g., hands-on use of Chimera volume visualization tools) * Date(s) * Location * RBVI staff involved * Hours of instruction (includes lectures, labs, and prep time) * Number of attendees * Comments/remarks/related URLs (e.g., students brought their own data sets for analysis) --------------------------------------------------------------------------- 2010/2011 report --------------------------------------------------------------------------- June 9, 2010 Demonstration showing DNA for 13 students age 8 from Celsius and Beyond summer science camp. Organized with Auritte Cohen-Ross. Showed light microscopy volume time series of chromosomes in dividing cells, electron microscopy of chromosomes, DNA molecular structure, nucleosomes and chromatin (http://www.cgl.ucsf.edu/chimera/dna-jun2010/dnademo.html). 8 hours preparation. 1 hour demonstration in RBVI visualization room. Many questions from kids "What happens if you eat a bubble?". - Tom Goddard July 11, 2010 Presentation on Cytoscape at ISMB 2010 to an audience of approximately 60. The presentation provided an introduction to Cytoscape's capabilities and some of the new features in Cytoscape 2.7 along with some new and recently enhanced plugins. - Scooter Morris July 13, 2010 "Network visualization and analysis using Cytoscape" Birds of a Feather session at ISMB 2010. Scooter Morris facilitated this session to solicit input from Cytoscape users and developers. About 30 participants. July 18, 2010 "Cytoscape User Tutorial". 2 hour introductory user tutorial given to about 50 users as part of the annual Cytoscape Retreat. - Scooter Morris July 18, 2010 Plugin demonstration on CyCommandHandlers as part of the Cytoscape Retreat to about 100 participants. - Scooter Morris August 16, 2010 Tutorial given at CSB 2010: "Analysis and Visualization of Biological Networks". This was a 1/2 day tutorial given to 15 participants that covered visualization and analytical approaches to understanding biological networks. Second half of tutorial introduced Cytoscape as a tool and provided a hands-on exercise. - Scooter Morris September 29, 2010 40-minute presentation to ~14 students in UCSF BP204, "Macromolecular Interactions and Assemblies" class. Included 5 min on history of Computer Graphics Lab, the remainder a Chimera demonstration: basic usage, morphing, viewing sequences, showing attribute values, building multimers, stereo. Prep time 12 hours including updating the previous year's presentation, testing with the current version of Chimera, rehearsing. - Elaine Meng, Eric Pettersen September 29, 2010 30-minute presentation to ~50 attendees, then followed by 90-minute tutorial to ~20 students at Department of Computational and System Biology, School of Medicine and Clinical Translational Science Institute, University of Pittsburgh. The presentation part, titled "Introduction to UCSF Chimera, an Extensible Molecular Modeling System", covered the brief history of molecular visualization, RBVI history and Chimera highlighted features. The tutorial part went over several basic examples in the "getting started" document. Prep time 40 hours. - YZ (Zheng Yang) October 12-13, 2010 Poster presentation on segmentation and measurement of bacteria in termite gut at NIH workshop "Recent Advances and Future Prospects for Visualizing Macromolecular Complexes and Cellular Structures". 170 participants. 12 hours preparation. Discussions of research projects with about 10 attendees https://conferences.niaid.nih.gov/vbbethesda/ - Tom Goddard October 27, 2010 45-minute Chimera teaching demonstration to ~30 students for a graduate course in protein engineering at UC Berkeley (taught by Danielle Tullman-Ercek, Asst. Professor, Dept. of Chemical and Biomolecular Engineering, UC Berkeley). Covered basic usage, finding H-bonds, morphing, saving trajectories as movies, viewing sequences, showing attribute values, evaluating rotamers, performing virtual mutations, building multimers, and using stereo. Prep time 20 hours including adding more material to the previously developed demo, testing with the current version of Chimera, and rehearsing. - Elaine Meng, Eric Pettersen November 18, 2010 Two 45-minute demonstrations showing termite gut and OpcA meningitis bacterium protein to SMART team Lincoln high school students. This is a UCSF Science and Health Education Partnership (SEP) program. Showed FIBSEM data, spirochetes, flagella, handedness, endo-flagella, protein morphing, hydrophobic and electrostatic surface coloring to identify transmembrane and binding regions. 16 students. 6 hours preparation. - Tom Goddard December 2010 Chimera used to create image for RBVI holiday card: glutamine synthetase 12-mer styled as an "architectural plan" (black outlines around transparent ribbons on aged parchment background). Estimated 36 person-hours of work (including preparing candidate images, voting, format converting). - YZ (Zheng Yang) December 2, 2010 Two 45-minute demonstrations showing termite gut and OpcA meningitis bacterium protein to SMART team Galileo high school students. This is a UCSF Science and Health Education Partnership (SEP) program. Showed FIBSEM data, spirochetes, flagella, handedness, endo-flagella, protein morphing, hydrophobic and electrostatic surface coloring to identify transmembrane and binding regions. 20 students. 4 hours preparation. - Tom Goddard December 8, 2010 Two hour discussion and Chimera demonstration of myosin thick filament regulation for UCSF Tetrad graduate program macromolecules discussion group. Looked at thick filament architecture and myosin 2 heavy and light chain atomic models using stereo 3d visualization. 5 graduate students, led by professor Zev Gartner. 8 hours preparation. - Tom Goddard December 13, 2010 Chimera Release Party and RBVI Open House (2-5 pm in Genentech Hall N453, UCSF Mission Bay) for local researchers and students to meet the Chimera developers, see demonstrations and discuss features, tour the RBVI facilities, and share refreshments. Estimated 50 attendees, 3 hours for the event, 24 person-hours preparation, publicity, and cleanup. - Chimera team February 11, 2011 Demonstration showing immune system structures to 7 visiting candidate UCSF graduate students. West Nile virus with bound antibodies, cytotoxic T-cell EM data. Also showed 3d printer and plastic molecular models. Two 35 minute demonstrations. 4 hours preparation. - Tom Goddard February 11, 2011 Seminar at University of Toronto covering base cytoscape and RBVI plugins to group of about 50. The seminary was 2 hours and included introductory topics as well as some advanced discussion. 10 hours preparation - Scooter Morris --------------------------------------------------------------------------- [wiki:COT10 2009/2010 report] [wiki:COT09 2008/2009 report] ---------------------------------------------------------------------------