---- "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) ---- 2016/2017 report ---- May 30-June 4, 2016 Faculty at the EMBO Practical Course on Protein-Protein Interactions. A week-long master course funded by the European Molecular Biology Organization held at the Eötvös Loránd University in Budapest, Hungary. Taught sections on Cytoscape as well as Chimera and worked directly with a number of participants on their visualization and analysis challenges. 24 students, 16 hours preparation. * Scooter Morris June 5-8, 2016 [http://sites.psu.edu/bioinorganic/2016-bioinorganic-workshop Pennsylvania State Bioinorganic Workshop]. Two 4 hour hands-on workshops on using sequence similarity networks to aid in target selection, analyze metagenomics data, find and explore "linker" sequences, and explore genomic context. Approximately 20 attendees at each workshop. Approximately 1 week preparation + 8 hours teaching. * Shoshana Brown, Patsy Babbitt June 6-7, 2016 2 Day Ph.D. course offered at the Eötvös Loránd University in Budapest, Hungary. This was a shortened version of the 6 day course given the week before, but given for credit and pitched to a Ph.D. audience (although faculty were in attendance). Students were required to complete an assignment at the end of the course demonstrating their ability to combine network and structural analyses to investigate biological function. 30 participants, 8 hours preparation. * Scooter Morris June 14, 2016 Zika virus Chimera demonstration for 18 San Francisco high school students taking part in the [http://sep-sfhi.ucsf.edu UCSF Public Health Investigators] 4 week program. Showed 3d printing, cryoEM and atomic models, protein structure, crawling neutrophils, stereo visualization and oculus rift virtual reality. Two 45 minute demonstrations. 8 hours preparation. * Tom Goddard July 29, 2016 Introduction to network visualization and analysis with Cytoscape workshop given at the University of Southern Denmark in Odense, Denmark. 4 hours preparation. Estimated 20 attendees. * Scooter Morris August 15-16, 2016 Two day workshop at the University of Colorado, Boulder. Day 1 focused on structural visualization and analysis with UCSF Chimera and day 2 focused on network visualization and analysis with Cytoscape. 20 participants. * Scooter Morris September 1-2, 2016 Extended 2 day Cytoscape workshop for the National Cancer Institute on the NIH campus. Total of 24 participants. 16 hours preparation * Scooter Morris October 10, 2016 Crawling neutrophil demo, virtual reality vive headset for 14 officers of University of California Extramural Funding Group. Organized by Michael Nordberg at UCSF. 45 minute demonstration, 3 hours preparation. * Tom Goddard October 30, 2016 Bay Area Science Festival, [http://www.bayareascience.org/event/explorer-days-virtual-reality-and-white-blood-cells white blood cells in virtual reality]. Show 6 kids, 5 adults 3d microscopy of crawling cells with stereo projector and Vive VR headset. Showed nuclear pore on Oculus VR headset. Showed CAT lab and EM/NMR facility. 90 minute tour. Organized by Kishore Hari. 8 hours prep (made Oculus / Space Navigator work on Windows). * Tom Goddard November 21, 2016 EMBO Conference: [https://www.embl.de/training/events/2016/HYB16-01/programme/index.html Molecular Machines: Integrative Structural and Molecular Biology], Heidelberg. Half-hour talk including ChimeraX demo [http://www.rbvi.ucsf.edu/home/tef/talks/MolecularMachines.html Visualization and Analysis Challenges of Large Biomolecular Complexes]. About 15 hours prep, 100 attendees. * Tom Ferrin January 31, 2017 [http://www.cgl.ucsf.edu/chimera/data/antibiotic-jan2017/antibiotic.html Ribosome antibiotic virtual reality demonstration] at Byer's Award reception, Genentech Hall Atrium. Showed 50 visitors antibiotic bound to E coli ribosome and antibiotic resistance mutations during 90 minute reception. Organized by Danica Fujimori. 10 hour preparation and presentation. * Tom Goddard February 10 and 17, 2017 Virtual reality demonstration for student applicants to UCSF iPQB program. Showed ribosome antibiotic and crawling neutrophil in collagen filaments. Two demonstrations, 12 students, 30 minutes each. 2 hours preparation. Organized by Rebecca Brown. * Tom Goddard March 7, 2017 Tour and virtual reality demonstration for UCSF STEM (science technology engineering and mathematics) Career Day for San Francisco high school students. Showed wet labs and 3d visualization of crawling neutrophil in collagen filaments and E coli ribosome antibiotic. Two tours, 90 minutes and 75 minutes, each with 8 students and 3 adults. 5 hours preparation and presentation. Organized by Jennifer Kaelin. * Tom Goddard March 20, 2017 Hands-on training [http://www.rbvi.ucsf.edu/chimera/data/wcpcw-mar2017/moviemaking.html Creating animations with UCSF ChimeraX] at the [http://www.biochem.utah.edu/hill/wcpcw.html West Coast Protein Crystallography Workshop] at Asilomar. Showed how to make spin, morph, density fit, and virtual reality movies. 80 participants, about 50 using ChimeraX on laptop computers. 30 hours preparation and delivery. Organized by Janet Iwasa, Heidi Schubert, Chris Hill. * Tom Goddard April 11, 2017 Structural Biology Grid ([https://sbgrid.org SBGrid]) webinar showing how to use ChimeraX for movie making with cryoEM structures [http://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html Slides]. 40 online participants. Video recorded and available on YouTube at [https://www.youtube.com/user/SBGridTV SBGridTV]. 20 hours preparation and delivery. Organized by Michelle Ottaviano, Peter Meyer, Jason Key. * Tom Goddard June 20-21, 2017 Two antibiotic resistance demonstrations for [http://sep-sfhi.ucsf.edu SF Health Investigators] summer program or high school students. Showed macrolide antibiotic resistance by phosphorylation, and ribosome methylation. 20 participants. 5 hours preparation and delivery. Organized by Jenna Bernard, Ben Koo and Rebecca Smith of UCSF [http://biochemistry2.ucsf.edu/programs/sep/ Science and Health Education Partnership]. * Tom Goddard July 19, 2017 Demonstration for 7 legislator staff members for federal and state house and senate members as part of UCSF 101 Day. Visitors included staff for Pelosi, Feinstein, Kamala Harris, Sheehy, Hill, and two others. Discussed clinical and basic research at UCSF. Showed HIV reverse transcriptase with tenofovir inhibitor, E. coli ribosome antibiotic resistance with virtual reality, and molecular playground K-12 education VR software. 3 hours preparation and delivery. Organized by Laura Lane, UCSF associate director for government relations, and Hannah Murphy. * Alan Brilliant, Tom Goddard August 1, 2017 Three one-hour hands-on virtual reality demonstrations, each for 7 [http://cosmos.ucdavis.edu/cluster8.htm COSMOS] summer high school students from UC Davis. Showed E. coli ribosome antibiotic resistance and molecular playground VR software. Organized by Scooter Morris including other lab tours in the labs of Al Burlingame, Nevan Krogan and Joe DeRisi. 16 hours preparation and delivery. * Scooter Morris, Alan Brilliant, Tom Goddard October 5, 2017 Light microscopy demo, measuring distances in mitochondria, cell surface coloring from fluorescent marker, virtual reality. 90 minute demonstration to 20 students, postdocs, and researchers at UCSF using 3D light microscopy organized by Dyche Mullins. 8 hours preparation and delivery. * Tom Goddard October 28, 2017 Demo on drug development for neuro-degenerative disease for 10 visitors during UCSF Campaign fund raiser. Showed P97 molecular machine involved in protein recycling on stereo projector and with virtual reality and plastic models. 30 hours preparation and delivery. Organized by Michelle Clark at UCSF in University Development and Alumni Relations. * Tom Goddard, Tom Ferrin, Michelle Arkin, Matt Jacobson October 29, 2017 Virtual reality booth for Bay Area Science Festival and the World Conference of Science Journalists at UCSF. Let about 50 people try VR small molecule interaction using Molecular Zoo over a 4 hour period. About 1/3 were young, age 5 - 10. Each person manipulated molecules for about 5 minutes. Organized by Nick Weiler from UCSF Public Affairs. 8 hours preparation and delivery. * Tom Goddard November 27-28, 2017 Provided a two-day training on protein-protein interactions that covered both Cytoscape and UCSF Chimera at the Max Planck Institute for the Biology of Aging in Cologne, Germany. 75 Students the first day (Cytoscape) and 60 students the second day (UCSF Chimera). * Scooter Morris November 29, 2017 Training 25 students in UCSF Biophysics 204A on NMR and EM experimental methods. Showed coloring HSP90 protein surface by chemical shift perturbations produced by adding ligand, and Python script writing to create attribute text files. Also presented ChimeraX virtual reality for ligand visualization. Two hour presentation, 5 hours preparation. Organized by John Gross and Jim Fraser. * Tom Goddard December 11, 2017 Training 25 students in UCSF Biophysics 204A on bound ligand visualization and EM fitting. Showed comparing HSP90 bound ligands, aligning, hydrogen bond display, fitting HSP90 into low resolution (15 Angstrom) negative stain map. wo hour presentation, 5 hours preparation. Organized by Daniel Asarnow, Jim Fraser, John Gross. * Tom Goddard January 17, 2018 Virtual reality demo showing zebrafish brain activity with 3d lightsheet microscopy at the Byer's Award reception at UCSF. Showed light microscopy data to about 30 guests from the general public and UCSF. 12 hours preparation, 1 hour presentation. Organized by Bo Huang. * Tom Goddard, Dan Xie January 19 and 26, 2018 Demonstration for UCSF iPQB student applications, 5 students for 30 minutes each day. Showed neutrophils light microscopy and ribosome antibiotics with virtual reality. 3 hours preparation and delivery. Organized by Rebecca Brown, UCSF Graduate Program Coordinator. * Tom Goddard March 7, 2018 Demonstration for [http://www.ccmi.org/san-francisco-stem-career-day UCSF STEM Career Day] to 20 SF high school students showing neutrophils, E coli antibiotic resistance, and the molecular zoo app in virtual reality. Two groups of 10, one hour each demo, 5 hours preparation and delivery. Organized by Jennifer Kaelin at UCSF Science Education Partnership (SEP). * Tom Goddard March 20, 2018 VR demos showing mutating a residue of scorpion toxin to a total of 15 staff members of UCSF department of pharmaceutical chemistry. Tried bond rotation, swapping amino acids and minimizing energy in VR. Three 20 minute demos, 3 hours preparation and delivery. Organized by JoAnne Williams and Matt Jacobson. * Tom Goddard ---- Past reports [wiki:COT16 2016], [wiki:COT15 2015], [wiki:COT14 2014], [wiki:COT13 2013], [wiki:COT12 2012], [wiki:COT11 2011], [wiki:COT10 2010], [wiki:COT09 2009], [wiki:COT08 2008], [wiki:COT07 2007] ----